Read the Docs build information Build id: 546151 Project: cyverse-foss Version: foss-2021-spring Commit: df6f085aeda5850d69b01b279c195c765bc2deb0 Date: 2021-01-29T18:08:11.842897Z State: finished Success: True [rtd-command-info] start-time: 2021-01-29T18:08:15.452966Z, end-time: 2021-01-29T18:08:18.258129Z, duration: 2, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:CyVerse-learning-materials/foss.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.113' (RSA) to the list of known hosts. [rtd-command-info] start-time: 2021-01-29T18:08:19.030424Z, end-time: 2021-01-29T18:08:19.468817Z, duration: 0, exit-code: 0 git checkout --force origin/foss-2021-spring Note: checking out 'origin/foss-2021-spring'. 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 df6f085 Update cyverse_rst_defined_substitutions.txt [rtd-command-info] start-time: 2021-01-29T18:08:19.875868Z, end-time: 2021-01-29T18:08:19.932224Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-01-29T18:08:21.906889Z, end-time: 2021-01-29T18:08:25.805941Z, duration: 3, 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/foss-2021-spring/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2021-spring/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-01-29T18:08:25.941648Z, end-time: 2021-01-29T18:08:26.962974Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2021-spring/lib/python3.7/site-packages (21.0) Collecting pip Downloading pip-21.0-py3-none-any.whl (1.5 MB) Downloading pip-20.3.4-py2.py3-none-any.whl (1.5 MB) [rtd-command-info] start-time: 2021-01-29T18:08:27.869740Z, end-time: 2021-01-29T18:08:37.001854Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir setuptools==41.0.1 docutils==0.14 mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 six commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 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-py3-none-any.whl (543 kB) Collecting mock==1.0.1 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idna-2.10-py2.py3-none-any.whl (58 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.4-py2.py3-none-any.whl (89 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-py3-none-any.whl size=23755 sha256=1f26d92dd3f4bdb270f15d13fc08c9a9b0de05e2139877db3d815bfff0fc0429 Stored in directory: /tmp/pip-ephem-wheel-cache-m5x9zquv/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 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-py3-none-any.whl size=491059 sha256=df2306b18386e68e710ab346758617ff474e7e49519d938483c81e0b6bc1baca Stored in directory: /tmp/pip-ephem-wheel-cache-m5x9zquv/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock Attempting uninstall: setuptools Found existing installation: setuptools 52.0.0 Uninstalling setuptools-52.0.0: Successfully uninstalled setuptools-52.0.0 Successfully installed Jinja2-2.11.2 MarkupSafe-1.1.1 Pygments-2.7.4 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.8 pillow-5.4.1 pyparsing-2.4.7 pytz-2020.5 readthedocs-sphinx-ext-2.1.3 recommonmark-0.5.0 requests-2.25.1 setuptools-41.0.1 six-1.15.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.3 [rtd-command-info] start-time: 2021-01-29T18:08:38.833934Z, end-time: 2021-01-29T18:08:38.901935Z, 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 Learning: Foundational Open Science Skills 2021' copyright = '2021, CyVerse' author = 'CyVerse' version = 'spring-2021' release = 'spring-2021' epub_title = 'CyVerse Learning Foundations of Open Science Skills 2021' epub_author = ' Meghan Balk, Ryan Bartleme, Amanda Cooksey, Tina Lee, Sateesh Peri, Mary Margaret Sprinkle, Tyson L. Swetnam, Reetu Tuteja, Ramona L. Walls, Jason Williams' epub_publisher = 'CyVerse' epub_copyright = 'CC0 - Open Source' ########################################################################### # 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': "foss-2021-spring", 'version_slug': "foss-2021-spring", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", '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': [ ("pdf", "//learning.cyverse.org/_/downloads/foss/en/foss-2021-spring/pdf/"), ("html", "//learning.cyverse.org/_/downloads/foss/en/foss-2021-spring/htmlzip/"), ("epub", "//learning.cyverse.org/_/downloads/foss/en/foss-2021-spring/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-foss', 'name': u'foss', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://learning.cyverse.org/projects/foss/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'CyVerse-learning-materials', 'proxied_api_host': '/_', 'github_repo': 'foss', 'github_version': 'foss-2021-spring', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'foss-2021-spring', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'foss-2021-spring', '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': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'df6f085a', } # 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/546151/' 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: 2021-01-29T18:08:39.699330Z, end-time: 2021-01-29T18:08:46.319766Z, duration: 6, exit-code: 0 python -m sphinx -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 49 source files that are out of date updating environment: 49 added, 0 changed, 0 removed reading sources... 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[100%] software_essentials/linux /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2021-spring/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/foss-2021-spring/.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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/introtocontainers.rst:179: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **Accessing Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:52: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:136: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:37: WARNING: Title level inconsistent: **Find an app by** `searching `_ """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:40: WARNING: Title level inconsistent: **Browse by operation** """""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:45: WARNING: Title level inconsistent: **Find apps by community** """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:93: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:10: WARNING: Title underline too short. **Discovery Environment - Data Management** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:16: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:54: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:80: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:100: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:8: WARNING: Title underline too short. **Discovery Environment - Tools & Apps** ===================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:83: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:120: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:10: WARNING: Title underline too short. **Discovery Environment - VICE** ======== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:173: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:10: WARNING: Title underline too short. **Creating Workflows** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:104: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:106: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:24: WARNING: Unknown target name: "fair guiding principles". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmtools.rst:9: WARNING: Title underline too short. **Data Management Tools** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:84: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:58: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:50: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 2 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Tool/Software - Notes - Link * - A Second Monitor (highly recommended) - Having two monitors enables you to full-screen stream the instructional portion of the course while working on a second screen. This is particularly helpful if you currently only have a laptop screen. - * - SSH Clients (Windows) - PuTTY allows SSH connection to a remote machine, and is designed for Windows users who do not have a Mac/Linux terminal. MobaXterm is a single Windows application that provides a ton of functions for programmers, webmasters, IT administrators, and anybody is looking to manage system remotely - - `Download PuTTY `_ - `Download mobaXterm `_ - `Install Windows Subsystem for Linux (WSL) 2 `_ * - Text Editors - There is no 'best' text editor, but some are easier to use than others. Do some reading and pick one. - - `Atom `_ - `SublimeText `_ - `VisualStudioCode `_ - `Vim `_ - `Emacs `_ - `Nano `_ * - Cyberduck - Cyberduck is a third-party tool for uploading/downloading data to the CyVerse Data Store. Currently, this tool is available for Windows/MacOS only. You will need to download Cyberduck and the connection profile. We will go through configuration and installation during FOSS Onboarding. - - `Download Cyberduck `_ - `Installation for CyVerse `_ * - iCommands - iCommands are third-party software for command-line connection to the CyVerse Data Store. - Download and installation instructions available at `CyVerse Learning Center `__ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/main.rst:9: WARNING: Title underline too short. **Before FOSS Starts** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:511: WARNING: image file not readable: cloud_comput/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/intro.rst:10: WARNING: Title underline too short. **Introduction to Cloud Computing** =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/colab_culture.rst:10: WARNING: Title underline too short. **Collaboration Culture and Roles** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/instructors.rst:36: WARNING: Title underline too short. **CyVerse Staff** --------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:9: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:24: WARNING: Title underline too short. **Learning Objectives** ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:41: WARNING: Title underline too short. **Approach** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Introductory Activity** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:22: WARNING: Title underline too short. **Planning your own Open Science lab** """""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:9: WARNING: Title underline too short. **Schedule** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:141: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (2 vs 4). .. list-table:: :header-rows: 1 * - Time - Activity (Instructor) - Content - Expected Outcomes * - 0:00 - `Data Management Overview <../Data_management/overview.html>`_ - Organization, Sharing, Metadata - Understand why you need data management * - Guest Lecturer - Semantics, Ontologies, Metadata * - - `Data Management Tools <../Data_management/dmtools.html>`_ (Walls) - Open Science Framework, Protocols.io, CyVerse DataCommons - Creating data management plans, work with metadata * - - Homework for Week 5: `Data Management Plans <../Data_management/dmp.html>`_ (Walls) - Writing a Data Management Plan - Learn how to write an excellent DMP! /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ cyverse_rst_defined_substitutions.txt:3: WARNING: Duplicate substitution definition name: "CyVerse User Portal". cyverse_rst_defined_substitutions.txt:7: WARNING: Duplicate substitution definition name: "Data Store". cyverse_rst_defined_substitutions.txt:11: WARNING: Duplicate substitution definition name: "Data Store Manual". cyverse_rst_defined_substitutions.txt:15: WARNING: Duplicate substitution definition name: "Data Store Guide". cyverse_rst_defined_substitutions.txt:19: WARNING: Duplicate substitution definition name: "Discovery Environment". cyverse_rst_defined_substitutions.txt:23: WARNING: Duplicate substitution definition name: "DE Manual". cyverse_rst_defined_substitutions.txt:27: WARNING: Duplicate substitution definition name: "Discovery Environment Guide". cyverse_rst_defined_substitutions.txt:31: WARNING: Duplicate substitution definition name: "Atmosphere". cyverse_rst_defined_substitutions.txt:35: WARNING: Duplicate substitution definition name: "Atmosphere Manual". cyverse_rst_defined_substitutions.txt:39: WARNING: Duplicate substitution definition name: "Atmosphere Guide". cyverse_rst_defined_substitutions.txt:43: WARNING: Duplicate substitution definition name: "BisQue". cyverse_rst_defined_substitutions.txt:47: WARNING: Duplicate substitution definition name: "BisQue Manual". cyverse_rst_defined_substitutions.txt:51: WARNING: Duplicate substitution definition name: "BisQue Guide". cyverse_rst_defined_substitutions.txt:55: WARNING: Duplicate substitution definition name: "DNA Subway". cyverse_rst_defined_substitutions.txt:59: WARNING: Duplicate substitution definition name: "DNA Subway Manual". cyverse_rst_defined_substitutions.txt:63: WARNING: Duplicate substitution definition name: "DNA Subway Guide". cyverse_rst_defined_substitutions.txt:67: WARNING: Duplicate substitution definition name: "Agave API". cyverse_rst_defined_substitutions.txt:71: WARNING: Duplicate substitution definition name: "Agave Live Docs". cyverse_rst_defined_substitutions.txt:75: WARNING: Duplicate substitution definition name: "Agave Guide". cyverse_rst_defined_substitutions.txt:79: WARNING: Duplicate substitution definition name: "SciApps". cyverse_rst_defined_substitutions.txt:83: WARNING: Duplicate substitution definition name: "SciApps Manual". cyverse_rst_defined_substitutions.txt:87: WARNING: Duplicate substitution definition name: "SciApps Guide". cyverse_rst_defined_substitutions.txt:91: WARNING: Duplicate substitution definition name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:110: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:114: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:118: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:122: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:10: WARNING: Title underline too short. Foundations of Open Science Skills 2021 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:182: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:187: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:34: WARNING: Unknown directive type "Goals". .. Goals:: - Feel comfortable using the GitHub environment - Integrate at least one repository onto GitHub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:40: WARNING: Unknown directive type "Prerequisites". .. Prerequisites:: In order to complete this exercise you should have already installed ``git`` for the command line (`instructions `_) & created an account on the `GitHub `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:192: WARNING: Unknown directive type "Exercise". .. Exercise:: Create a new issue and relate it back to the issue you just created. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:349: WARNING: Unknown directive type "Definitions". .. Definitions:: **Git** - tool for version control. **GitHub** - hosted server that is also interactive. **repo** - short for repository; GitHub lets you create a remote repository online. **local** - on your personal computer. **clone** - copy of a repository that lives locally on your computer. Pushing changes will affect the repository online. **fetch** - getting latest changes to the repository on your local computer. **branch** - parallel to the master branch; allows you to make changes without affecting the master branch. Changes made on a branch can be merged back to the master. **fork** - copy of someone else's repository stored locally on your account. From forks, you can make pull requests to the master branch. **upstream** - primary or master branch of original repository. **downstream** - branch or fork of repository. **untracked** - changes made locally but not yet commited or pushed to the online repo. **staged** - item added to the repo. **commit** - finalize a change. **push** - add changes back to the remote repository. **merge** - takes changes from a branch or fork and applies them to the master. **pull request** - proposed changes to/within a repository. **issue** - suggestions or tasks needed for the repository. Allows you to track decisions, bugs with the repository, etc. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:432: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:410: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Title underline too short. **CI/CD** ====== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:30: WARNING: Title underline too short. **Continuous Development** ~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:71: WARNING: Title underline too short. **When to use CI?** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:107: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:106: WARNING: Title level inconsistent: *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:22: WARNING: Unknown directive type "remember". .. remember:: **SLACK** - Slack has `plenty of apps `_ for coordinating multiple services, i.e. Calendars, Github, GoogleDrive, Box, etc. - Slack is limiting unless you're willing to pay for the professional support. **Microsoft Teams** - Teams is used by many R1 research universities as part of their campus wide license agreement for Office 365 Business and Education. **Gitter** - Native integration with Github or Gitlab - Uses your GitHub username or Twitter handle for all Gitters you're a part of /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:39: WARNING: Title underline too short. *Other popular alternatives* """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:53: WARNING: Title underline too short. *Create a SLACK Workspace* ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:66: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: reproducible_science/./img/intercom.png cyverse_rst_defined_substitutions.txt:102: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:210: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 33 supplied. .. code-block:: bash $ ls -l total 576 drwxr-xr-x 7 amcooksey iplant-everyone 4096 Aug 7 20:14 data-shell -rw-r--r-- 1 amcooksey iplant-everyone 580102 Jan 29 10:54 data-shell.zip -rwxr-xr-x 1 amcooksey root 201 Jan 29 10:02 kanki.desktop /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:217: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 81 supplied. .. code-block:: bash $ cd data-shell $ ls -l total 52 drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 21:51 creatures drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 data drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 20:13 molecules drwxr-xr-x 3 amcooksey iplant-everyone 4096 Aug 7 20:13 north-pacific-gyre -rw-r--r-- 1 amcooksey iplant-everyone 86 Aug 7 20:13 notes.txt -rw-r--r-- 1 amcooksey iplant-everyone 32 Aug 7 20:13 pizza.cfg -rw-r--r-- 1 amcooksey iplant-everyone 21583 Aug 7 20:13 solar.pdf drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 writing /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:743: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:748: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:681: WARNING: Undefined substitution referenced: "nano>>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:746: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:622: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:59: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: 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[100%] software_essentials/linux /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2021-spring/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/foss-2021-spring/.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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/introtocontainers.rst:179: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **Accessing Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:52: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:136: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:37: WARNING: Title level inconsistent: **Find an app by** `searching `_ """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:40: WARNING: Title level inconsistent: **Browse by operation** """""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:45: WARNING: Title level inconsistent: **Find apps by community** """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:93: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:10: WARNING: Title underline too short. **Discovery Environment - Data Management** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:16: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:54: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:80: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:100: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:8: WARNING: Title underline too short. **Discovery Environment - Tools & Apps** ===================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:83: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:120: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:10: WARNING: Title underline too short. **Discovery Environment - VICE** ======== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:173: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:10: WARNING: Title underline too short. **Creating Workflows** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:104: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:106: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:24: WARNING: Unknown target name: "fair guiding principles". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmtools.rst:9: WARNING: Title underline too short. **Data Management Tools** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:84: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:58: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:50: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 2 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Tool/Software - Notes - Link * - A Second Monitor (highly recommended) - Having two monitors enables you to full-screen stream the instructional portion of the course while working on a second screen. This is particularly helpful if you currently only have a laptop screen. - * - SSH Clients (Windows) - PuTTY allows SSH connection to a remote machine, and is designed for Windows users who do not have a Mac/Linux terminal. MobaXterm is a single Windows application that provides a ton of functions for programmers, webmasters, IT administrators, and anybody is looking to manage system remotely - - `Download PuTTY `_ - `Download mobaXterm `_ - `Install Windows Subsystem for Linux (WSL) 2 `_ * - Text Editors - There is no 'best' text editor, but some are easier to use than others. Do some reading and pick one. - - `Atom `_ - `SublimeText `_ - `VisualStudioCode `_ - `Vim `_ - `Emacs `_ - `Nano `_ * - Cyberduck - Cyberduck is a third-party tool for uploading/downloading data to the CyVerse Data Store. Currently, this tool is available for Windows/MacOS only. You will need to download Cyberduck and the connection profile. We will go through configuration and installation during FOSS Onboarding. - - `Download Cyberduck `_ - `Installation for CyVerse `_ * - iCommands - iCommands are third-party software for command-line connection to the CyVerse Data Store. - Download and installation instructions available at `CyVerse Learning Center `__ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/main.rst:9: WARNING: Title underline too short. **Before FOSS Starts** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:511: WARNING: image file not readable: cloud_comput/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/intro.rst:10: WARNING: Title underline too short. **Introduction to Cloud Computing** =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/colab_culture.rst:10: WARNING: Title underline too short. **Collaboration Culture and Roles** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/instructors.rst:36: WARNING: Title underline too short. **CyVerse Staff** --------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:9: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:24: WARNING: Title underline too short. **Learning Objectives** ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:41: WARNING: Title underline too short. **Approach** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Introductory Activity** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:22: WARNING: Title underline too short. **Planning your own Open Science lab** """""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:9: WARNING: Title underline too short. **Schedule** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:141: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (2 vs 4). .. list-table:: :header-rows: 1 * - Time - Activity (Instructor) - Content - Expected Outcomes * - 0:00 - `Data Management Overview <../Data_management/overview.html>`_ - Organization, Sharing, Metadata - Understand why you need data management * - Guest Lecturer - Semantics, Ontologies, Metadata * - - `Data Management Tools <../Data_management/dmtools.html>`_ (Walls) - Open Science Framework, Protocols.io, CyVerse DataCommons - Creating data management plans, work with metadata * - - Homework for Week 5: `Data Management Plans <../Data_management/dmp.html>`_ (Walls) - Writing a Data Management Plan - Learn how to write an excellent DMP! /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ cyverse_rst_defined_substitutions.txt:3: WARNING: Duplicate substitution definition name: "CyVerse User Portal". cyverse_rst_defined_substitutions.txt:7: WARNING: Duplicate substitution definition name: "Data Store". cyverse_rst_defined_substitutions.txt:11: WARNING: Duplicate substitution definition name: "Data Store Manual". cyverse_rst_defined_substitutions.txt:15: WARNING: Duplicate substitution definition name: "Data Store Guide". cyverse_rst_defined_substitutions.txt:19: WARNING: Duplicate substitution definition name: "Discovery Environment". cyverse_rst_defined_substitutions.txt:23: WARNING: Duplicate substitution definition name: "DE Manual". cyverse_rst_defined_substitutions.txt:27: WARNING: Duplicate substitution definition name: "Discovery Environment Guide". cyverse_rst_defined_substitutions.txt:31: WARNING: Duplicate substitution definition name: "Atmosphere". cyverse_rst_defined_substitutions.txt:35: WARNING: Duplicate substitution definition name: "Atmosphere Manual". cyverse_rst_defined_substitutions.txt:39: WARNING: Duplicate substitution definition name: "Atmosphere Guide". cyverse_rst_defined_substitutions.txt:43: WARNING: Duplicate substitution definition name: "BisQue". cyverse_rst_defined_substitutions.txt:47: WARNING: Duplicate substitution definition name: "BisQue Manual". cyverse_rst_defined_substitutions.txt:51: WARNING: Duplicate substitution definition name: "BisQue Guide". cyverse_rst_defined_substitutions.txt:55: WARNING: Duplicate substitution definition name: "DNA Subway". cyverse_rst_defined_substitutions.txt:59: WARNING: Duplicate substitution definition name: "DNA Subway Manual". cyverse_rst_defined_substitutions.txt:63: WARNING: Duplicate substitution definition name: "DNA Subway Guide". cyverse_rst_defined_substitutions.txt:67: WARNING: Duplicate substitution definition name: "Agave API". cyverse_rst_defined_substitutions.txt:71: WARNING: Duplicate substitution definition name: "Agave Live Docs". cyverse_rst_defined_substitutions.txt:75: WARNING: Duplicate substitution definition name: "Agave Guide". cyverse_rst_defined_substitutions.txt:79: WARNING: Duplicate substitution definition name: "SciApps". cyverse_rst_defined_substitutions.txt:83: WARNING: Duplicate substitution definition name: "SciApps Manual". cyverse_rst_defined_substitutions.txt:87: WARNING: Duplicate substitution definition name: "SciApps Guide". cyverse_rst_defined_substitutions.txt:91: WARNING: Duplicate substitution definition name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:110: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:114: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:118: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:122: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:10: WARNING: Title underline too short. Foundations of Open Science Skills 2021 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:182: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:187: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:34: WARNING: Unknown directive type "Goals". .. Goals:: - Feel comfortable using the GitHub environment - Integrate at least one repository onto GitHub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:40: WARNING: Unknown directive type "Prerequisites". .. Prerequisites:: In order to complete this exercise you should have already installed ``git`` for the command line (`instructions `_) & created an account on the `GitHub `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:192: WARNING: Unknown directive type "Exercise". .. Exercise:: Create a new issue and relate it back to the issue you just created. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:349: WARNING: Unknown directive type "Definitions". .. Definitions:: **Git** - tool for version control. **GitHub** - hosted server that is also interactive. **repo** - short for repository; GitHub lets you create a remote repository online. **local** - on your personal computer. **clone** - copy of a repository that lives locally on your computer. Pushing changes will affect the repository online. **fetch** - getting latest changes to the repository on your local computer. **branch** - parallel to the master branch; allows you to make changes without affecting the master branch. Changes made on a branch can be merged back to the master. **fork** - copy of someone else's repository stored locally on your account. From forks, you can make pull requests to the master branch. **upstream** - primary or master branch of original repository. **downstream** - branch or fork of repository. **untracked** - changes made locally but not yet commited or pushed to the online repo. **staged** - item added to the repo. **commit** - finalize a change. **push** - add changes back to the remote repository. **merge** - takes changes from a branch or fork and applies them to the master. **pull request** - proposed changes to/within a repository. **issue** - suggestions or tasks needed for the repository. Allows you to track decisions, bugs with the repository, etc. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:432: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:410: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Title underline too short. **CI/CD** ====== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:30: WARNING: Title underline too short. **Continuous Development** ~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:71: WARNING: Title underline too short. **When to use CI?** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:107: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:106: WARNING: Title level inconsistent: *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:22: WARNING: Unknown directive type "remember". .. remember:: **SLACK** - Slack has `plenty of apps `_ for coordinating multiple services, i.e. Calendars, Github, GoogleDrive, Box, etc. - Slack is limiting unless you're willing to pay for the professional support. **Microsoft Teams** - Teams is used by many R1 research universities as part of their campus wide license agreement for Office 365 Business and Education. **Gitter** - Native integration with Github or Gitlab - Uses your GitHub username or Twitter handle for all Gitters you're a part of /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:39: WARNING: Title underline too short. *Other popular alternatives* """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:53: WARNING: Title underline too short. *Create a SLACK Workspace* ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:66: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: reproducible_science/./img/intercom.png cyverse_rst_defined_substitutions.txt:102: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:210: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 33 supplied. .. code-block:: bash $ ls -l total 576 drwxr-xr-x 7 amcooksey iplant-everyone 4096 Aug 7 20:14 data-shell -rw-r--r-- 1 amcooksey iplant-everyone 580102 Jan 29 10:54 data-shell.zip -rwxr-xr-x 1 amcooksey root 201 Jan 29 10:02 kanki.desktop /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:217: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 81 supplied. .. code-block:: bash $ cd data-shell $ ls -l total 52 drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 21:51 creatures drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 data drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 20:13 molecules drwxr-xr-x 3 amcooksey iplant-everyone 4096 Aug 7 20:13 north-pacific-gyre -rw-r--r-- 1 amcooksey iplant-everyone 86 Aug 7 20:13 notes.txt -rw-r--r-- 1 amcooksey iplant-everyone 32 Aug 7 20:13 pizza.cfg -rw-r--r-- 1 amcooksey iplant-everyone 21583 Aug 7 20:13 solar.pdf drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 writing /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:743: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:748: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:681: WARNING: Undefined substitution referenced: "nano>>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:746: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:622: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:59: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". 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[100%] software_essentials/linux /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2021-spring/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/foss-2021-spring/.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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/introtocontainers.rst:179: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **Accessing Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:52: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:136: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:37: WARNING: Title level inconsistent: **Find an app by** `searching `_ """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:40: WARNING: Title level inconsistent: **Browse by operation** """""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:45: WARNING: Title level inconsistent: **Find apps by community** """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:93: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:10: WARNING: Title underline too short. **Discovery Environment - Data Management** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:16: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:54: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:80: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:100: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:8: WARNING: Title underline too short. **Discovery Environment - Tools & Apps** ===================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:83: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:120: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:10: WARNING: Title underline too short. **Discovery Environment - VICE** ======== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:173: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:10: WARNING: Title underline too short. **Creating Workflows** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:104: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:106: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:24: WARNING: Unknown target name: "fair guiding principles". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmtools.rst:9: WARNING: Title underline too short. **Data Management Tools** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:84: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:58: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:50: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 2 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Tool/Software - Notes - Link * - A Second Monitor (highly recommended) - Having two monitors enables you to full-screen stream the instructional portion of the course while working on a second screen. This is particularly helpful if you currently only have a laptop screen. - * - SSH Clients (Windows) - PuTTY allows SSH connection to a remote machine, and is designed for Windows users who do not have a Mac/Linux terminal. MobaXterm is a single Windows application that provides a ton of functions for programmers, webmasters, IT administrators, and anybody is looking to manage system remotely - - `Download PuTTY `_ - `Download mobaXterm `_ - `Install Windows Subsystem for Linux (WSL) 2 `_ * - Text Editors - There is no 'best' text editor, but some are easier to use than others. Do some reading and pick one. - - `Atom `_ - `SublimeText `_ - `VisualStudioCode `_ - `Vim `_ - `Emacs `_ - `Nano `_ * - Cyberduck - Cyberduck is a third-party tool for uploading/downloading data to the CyVerse Data Store. Currently, this tool is available for Windows/MacOS only. You will need to download Cyberduck and the connection profile. We will go through configuration and installation during FOSS Onboarding. - - `Download Cyberduck `_ - `Installation for CyVerse `_ * - iCommands - iCommands are third-party software for command-line connection to the CyVerse Data Store. - Download and installation instructions available at `CyVerse Learning Center `__ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/main.rst:9: WARNING: Title underline too short. **Before FOSS Starts** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:511: WARNING: image file not readable: cloud_comput/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/intro.rst:10: WARNING: Title underline too short. **Introduction to Cloud Computing** =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/colab_culture.rst:10: WARNING: Title underline too short. **Collaboration Culture and Roles** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/instructors.rst:36: WARNING: Title underline too short. **CyVerse Staff** --------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:9: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:24: WARNING: Title underline too short. **Learning Objectives** ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:41: WARNING: Title underline too short. **Approach** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Introductory Activity** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:22: WARNING: Title underline too short. **Planning your own Open Science lab** """""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:9: WARNING: Title underline too short. **Schedule** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:141: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (2 vs 4). .. list-table:: :header-rows: 1 * - Time - Activity (Instructor) - Content - Expected Outcomes * - 0:00 - `Data Management Overview <../Data_management/overview.html>`_ - Organization, Sharing, Metadata - Understand why you need data management * - Guest Lecturer - Semantics, Ontologies, Metadata * - - `Data Management Tools <../Data_management/dmtools.html>`_ (Walls) - Open Science Framework, Protocols.io, CyVerse DataCommons - Creating data management plans, work with metadata * - - Homework for Week 5: `Data Management Plans <../Data_management/dmp.html>`_ (Walls) - Writing a Data Management Plan - Learn how to write an excellent DMP! /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ cyverse_rst_defined_substitutions.txt:3: WARNING: Duplicate substitution definition name: "CyVerse User Portal". cyverse_rst_defined_substitutions.txt:7: WARNING: Duplicate substitution definition name: "Data Store". cyverse_rst_defined_substitutions.txt:11: WARNING: Duplicate substitution definition name: "Data Store Manual". cyverse_rst_defined_substitutions.txt:15: WARNING: Duplicate substitution definition name: "Data Store Guide". cyverse_rst_defined_substitutions.txt:19: WARNING: Duplicate substitution definition name: "Discovery Environment". cyverse_rst_defined_substitutions.txt:23: WARNING: Duplicate substitution definition name: "DE Manual". cyverse_rst_defined_substitutions.txt:27: WARNING: Duplicate substitution definition name: "Discovery Environment Guide". cyverse_rst_defined_substitutions.txt:31: WARNING: Duplicate substitution definition name: "Atmosphere". cyverse_rst_defined_substitutions.txt:35: WARNING: Duplicate substitution definition name: "Atmosphere Manual". cyverse_rst_defined_substitutions.txt:39: WARNING: Duplicate substitution definition name: "Atmosphere Guide". cyverse_rst_defined_substitutions.txt:43: WARNING: Duplicate substitution definition name: "BisQue". cyverse_rst_defined_substitutions.txt:47: WARNING: Duplicate substitution definition name: "BisQue Manual". cyverse_rst_defined_substitutions.txt:51: WARNING: Duplicate substitution definition name: "BisQue Guide". cyverse_rst_defined_substitutions.txt:55: WARNING: Duplicate substitution definition name: "DNA Subway". cyverse_rst_defined_substitutions.txt:59: WARNING: Duplicate substitution definition name: "DNA Subway Manual". cyverse_rst_defined_substitutions.txt:63: WARNING: Duplicate substitution definition name: "DNA Subway Guide". cyverse_rst_defined_substitutions.txt:67: WARNING: Duplicate substitution definition name: "Agave API". cyverse_rst_defined_substitutions.txt:71: WARNING: Duplicate substitution definition name: "Agave Live Docs". cyverse_rst_defined_substitutions.txt:75: WARNING: Duplicate substitution definition name: "Agave Guide". cyverse_rst_defined_substitutions.txt:79: WARNING: Duplicate substitution definition name: "SciApps". cyverse_rst_defined_substitutions.txt:83: WARNING: Duplicate substitution definition name: "SciApps Manual". cyverse_rst_defined_substitutions.txt:87: WARNING: Duplicate substitution definition name: "SciApps Guide". cyverse_rst_defined_substitutions.txt:91: WARNING: Duplicate substitution definition name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:110: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:114: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:118: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:122: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:10: WARNING: Title underline too short. Foundations of Open Science Skills 2021 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:182: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:187: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:34: WARNING: Unknown directive type "Goals". .. Goals:: - Feel comfortable using the GitHub environment - Integrate at least one repository onto GitHub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:40: WARNING: Unknown directive type "Prerequisites". .. Prerequisites:: In order to complete this exercise you should have already installed ``git`` for the command line (`instructions `_) & created an account on the `GitHub `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:192: WARNING: Unknown directive type "Exercise". .. Exercise:: Create a new issue and relate it back to the issue you just created. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:349: WARNING: Unknown directive type "Definitions". .. Definitions:: **Git** - tool for version control. **GitHub** - hosted server that is also interactive. **repo** - short for repository; GitHub lets you create a remote repository online. **local** - on your personal computer. **clone** - copy of a repository that lives locally on your computer. Pushing changes will affect the repository online. **fetch** - getting latest changes to the repository on your local computer. **branch** - parallel to the master branch; allows you to make changes without affecting the master branch. Changes made on a branch can be merged back to the master. **fork** - copy of someone else's repository stored locally on your account. From forks, you can make pull requests to the master branch. **upstream** - primary or master branch of original repository. **downstream** - branch or fork of repository. **untracked** - changes made locally but not yet commited or pushed to the online repo. **staged** - item added to the repo. **commit** - finalize a change. **push** - add changes back to the remote repository. **merge** - takes changes from a branch or fork and applies them to the master. **pull request** - proposed changes to/within a repository. **issue** - suggestions or tasks needed for the repository. Allows you to track decisions, bugs with the repository, etc. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:432: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:410: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Title underline too short. **CI/CD** ====== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:30: WARNING: Title underline too short. **Continuous Development** ~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:71: WARNING: Title underline too short. **When to use CI?** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:107: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:106: WARNING: Title level inconsistent: *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:22: WARNING: Unknown directive type "remember". .. remember:: **SLACK** - Slack has `plenty of apps `_ for coordinating multiple services, i.e. Calendars, Github, GoogleDrive, Box, etc. - Slack is limiting unless you're willing to pay for the professional support. **Microsoft Teams** - Teams is used by many R1 research universities as part of their campus wide license agreement for Office 365 Business and Education. **Gitter** - Native integration with Github or Gitlab - Uses your GitHub username or Twitter handle for all Gitters you're a part of /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:39: WARNING: Title underline too short. *Other popular alternatives* """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:53: WARNING: Title underline too short. *Create a SLACK Workspace* ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:66: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: reproducible_science/./img/intercom.png cyverse_rst_defined_substitutions.txt:102: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:210: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 33 supplied. .. code-block:: bash $ ls -l total 576 drwxr-xr-x 7 amcooksey iplant-everyone 4096 Aug 7 20:14 data-shell -rw-r--r-- 1 amcooksey iplant-everyone 580102 Jan 29 10:54 data-shell.zip -rwxr-xr-x 1 amcooksey root 201 Jan 29 10:02 kanki.desktop /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:217: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 81 supplied. .. code-block:: bash $ cd data-shell $ ls -l total 52 drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 21:51 creatures drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 data drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 20:13 molecules drwxr-xr-x 3 amcooksey iplant-everyone 4096 Aug 7 20:13 north-pacific-gyre -rw-r--r-- 1 amcooksey iplant-everyone 86 Aug 7 20:13 notes.txt -rw-r--r-- 1 amcooksey iplant-everyone 32 Aug 7 20:13 pizza.cfg -rw-r--r-- 1 amcooksey iplant-everyone 21583 Aug 7 20:13 solar.pdf drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 writing /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:743: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:748: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:681: WARNING: Undefined substitution referenced: "nano>>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:746: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:622: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:59: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:56: WARNING: Title underline too short. *Package Managers* ~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:63: WARNING: Title underline too short. *Self Paced* ---------- looking for now-outdated files... none found pickling environment... done checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/.github/ISSUE_TEMPLATE/triage-for-2-0-release.md: 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/home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/about_cyverse.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/location.rst: WARNING: document isn't included in any toctree /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst: WARNING: document isn't included in any toctree done processing CyVerseDocumentation.tex...index before/main before/installation getting_started/schedule getting_started/instructors getting_started/glossary getting_started/intro getting_started/code_of_conduct getting_started/open_sci_lab getting_started/colab_culture software_essentials/commandline software_essentials/linux reproducible_science/intro reproducible_science/communication reproducible_science/GitHub reproducible_science/cicd reproducible_science/websites Data_management/overview Data_management/FAIR Data_management/dmp Data_management/dmtools CyVerse/intro_to_cyverse CyVerse/data_store CyVerse/de-data-manage CyVerse/de-data-analysis CyVerse/tool_integration_app_building_DE CyVerse/vice cloud_comput/intro cloud_comput/atmo cloud_comput/xsede cloud_comput/cyberinfrastructure Containers/introtocontainers Containers/dockeronatmo Containers/dockerintro Containers/dockeradvanced software_essentials/R_Studio software_essentials/RStudio_Git github_action/eht documentation/githubpages resolving references... /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:127: WARNING: a suitable image for latex builder not found: ['image/svg+xml'] (https://readthedocs.org/projects/pip/badge/?version=latest&style=flat) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:128: WARNING: a suitable image for latex builder not 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WARNING: Missing searchtools: /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/_build/latex/_static/searchtools.js [rtd-command-info] start-time: 2021-01-29T18:09:11.894764Z, end-time: 2021-01-29T18:09:11.953643Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2021-01-29T18:09:12.325695Z, end-time: 2021-01-29T18:09:58.577603Z, duration: 46, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-foss -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. 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Package pdftex.def Error: File `../img/cyverse_learning.png' not found: using draft setting. See the pdftex.def package documentation for explanation. Type H for immediate help. ... l.82 ...nxpxdimen]{{../img/cyverse_learning}.png}} ^^M (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) Overfull \hbox (132.49107pt too wide) in paragraph at lines 91--92 [][] [1 <./homeicon8.png>] [2 <./foss-main.png>] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3 <./cyverse_learni ng3.png> <./homeicon3.png>] [4 <./cyverse_globe_cmyk.png> <./Learningcenter_DkB lue1.png>] [5] Overfull \hbox (7.22351pt too wide) in paragraph at lines 357--357 []\T1/phv/m/n/10 Time| Overfull \hbox (2.78355pt too wide) in paragraph at lines 357--357 []\T1/ptm/m/n/10 0:00| Overfull \hbox (2.78355pt too wide) in paragraph at lines 357--357 []\T1/ptm/m/n/10 0:30| Overfull \hbox (2.78355pt too wide) in paragraph at lines 357--357 []\T1/ptm/m/n/10 1:00| Overfull \hbox (2.78355pt too wide) in paragraph at lines 357--357 []\T1/ptm/m/n/10 1:30| Underfull \hbox (badness 10000) in paragraph at lines 2--357 [][][]\T1/ptm/m/n/10 Cy-Verse Walk-through[][] Overfull \hbox (7.22351pt too wide) in paragraph at lines 404--404 []\T1/phv/m/n/10 Time| Overfull \hbox (2.78355pt too wide) in paragraph at lines 404--404 []\T1/ptm/m/n/10 0:00| Underfull \hbox (badness 10000) in paragraph at lines 404--404 []\T1/ptm/m/n/10 Us-ing tools like Underfull \hbox (badness 10000) in paragraph at lines 404--404 \T1/ptm/m/n/10 Slack, Medium, Overfull \hbox (2.78355pt too wide) in paragraph at lines 404--404 []\T1/ptm/m/n/10 0:45| Underfull \hbox (badness 10000) in paragraph at lines 404--404 []\T1/ptm/m/n/10 Com-mu-ni-ca-tion & [6 <./cyverse_learning6.png> <./homeicon6.png>] Overfull \hbox (7.22351pt too wide) in paragraph at lines 451--451 []\T1/phv/m/n/10 Time| Overfull \hbox (2.78355pt too wide) in paragraph at lines 451--451 []\T1/ptm/m/n/10 0:00| Underfull \hbox (badness 10000) in paragraph at lines 451--451 []\T1/ptm/m/n/10 Un-der-stand-ing what Underfull \hbox (badness 10000) in paragraph at lines 451--451 \T1/ptm/m/n/10 open source sofware Overfull \hbox (2.78355pt too wide) in paragraph at lines 451--451 []\T1/ptm/m/n/10 1:00| Underfull \hbox (badness 10000) in paragraph at lines 451--451 \T1/ptm/m/n/10 I: [][]In-tro-duc-tion to Underfull \hbox (badness 10000) in paragraph at lines 451--451 []\T1/ptm/m/n/10 Un-der-stand-ing of [][]git[][] Overfull \hbox (7.22351pt too wide) in paragraph at lines 495--495 []\T1/phv/m/n/10 Time| Underfull \hbox (badness 10000) in paragraph at lines 495--495 []\T1/phv/m/n/10 Ex-pected Overfull \hbox (2.78355pt too wide) in paragraph at lines 495--495 []\T1/ptm/m/n/10 0:00| Underfull \hbox (badness 10000) in paragraph at lines 495--495 []\T1/ptm/m/n/10 Re-pro-ducible Re-search I: Launch-ing VMs Overfull \hbox (3.53508pt too wide) in paragraph at lines 543--543 []\T1/phv/m/n/10 Time| Underfull \hbox (badness 10000) in paragraph at lines 543--543 []\T1/phv/m/n/10 Ex-pected Out- Overfull \hbox (7.22351pt too wide) in paragraph at lines 588--588 []\T1/phv/m/n/10 Time| Overfull \hbox (2.78355pt too wide) in paragraph at lines 588--588 []\T1/ptm/m/n/10 0:00| [7] Overfull \hbox (6.53651pt too wide) in paragraph at lines 629--629 []\T1/phv/m/n/10 Time| Underfull \hbox (badness 10000) in paragraph at lines 629--629 []\T1/phv/m/n/10 Ex-pected Overfull \hbox (2.09656pt too wide) in paragraph at lines 629--629 []\T1/ptm/m/n/10 0:00| Overfull \hbox (2.09656pt too wide) in paragraph at lines 629--629 []\T1/ptm/m/n/10 1:00| Overfull \hbox (6.1672pt too wide) in paragraph at lines 674--674 []\T1/phv/m/n/10 Time| Underfull \hbox (badness 10000) in paragraph at lines 674--674 []\T1/phv/m/n/10 Ex-pected Out- Overfull \hbox (1.72725pt too wide) in paragraph at lines 674--674 []\T1/ptm/m/n/10 0:00| Overfull \hbox (1.72725pt too wide) in paragraph at lines 674--674 []\T1/ptm/m/n/10 1:00| [8] [9] [10] [11] [12] [13] [14] Overfull \hbox (293.20688pt too wide) in paragraph at lines 1310--1310 [] Underfull \hbox (badness 10000) in paragraph at lines 1310--1310 [15] [16] [17] [18] [19] [20 <./cyverse_learning9.png> <./homeicon10.png>] [21] Overfull \hbox (94.89604pt too wide) in paragraph at lines 1779--1780 [][] [22 <./cmd1.png (PNG copy)>] [23 <./cmd2.png (PNG copy)>] [24 <./cmd3.png (PNG copy)>] [25] [26] Overfull \hbox (94.88777pt too wide) in paragraph at lines 2059--2060 [][] [27 <./cmd15.png (PNG copy)>] [28] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [29] [30] [31] [32] [33] Package textcomp Warning: Symbol \textuparrow not provided by (textcomp) font family ptm in TS1 encoding. 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See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.3853 \end{tabulary} [49] [50] [51 <./cyverse_learning2.png> <./homeicon2.png>] [52] Overfull \hbox (26.27048pt too wide) in paragraph at lines 4105--4105 [] Underfull \hbox (badness 10000) in paragraph at lines 4105--4105 [53 <./data_life_cycle.png>] [54] [55] [56] [57] LaTeX Warning: Hyper reference `Data_management/FAIR:care-principles' on page 5 8 undefined on input line 4569. 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[169] [170] Chapter 3. No file cyverse-foss.ind. [171 <./intercom.png>] (./cyverse-foss.aux) Package rerunfilecheck Warning: File `cyverse-foss.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-s uper-ts1.enc} Output written on cyverse-foss.pdf (175 pages, 10785497 bytes). Transcript written on cyverse-foss.log. Latexmk: Index file 'cyverse-foss.idx' was written Latexmk: Missing input file: '{../img/cyverse_learning}.png' from line 'LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.' Latexmk: Missing input file: '{reproducible_science/./img/intercom}.png' from line 'LaTeX Warning: File `{reproducible_science/./img/intercom}.png' not found on in' Latexmk: Missing input file: '{reproducible_science/./img/intercom}.png' from line 'LaTeX Warning: File `{reproducible_science/./img/intercom}.png' not found on input line 2833.' Latexmk: Missing input file: '{cloud_comput/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{cloud_comput/../img/notebook_terminal}.png' not found on ' Latexmk: Missing input file: '{cloud_comput/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{cloud_comput/../img/notebook_terminal}.png' not found on input line 6686.' Latexmk: Missing input file: 'cyverse-foss.ind' from line 'No file cyverse-foss.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-foss.pdf' Rule 'makeindex cyverse-foss.idx': File changes, etc: Non-existent destination files: 'cyverse-foss.ind' ------------ Run number 1 of rule 'makeindex cyverse-foss.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-foss.ind" "cyverse-foss.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-foss.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file cyverse-foss.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-foss.ind. Transcript written in cyverse-foss.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-foss.aux' 'cyverse-foss.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-foss" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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[169] [170] Chapter 3. (./cyverse-foss.ind) [171 <./intercom.png>] (./cyverse-foss.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-s uper-ts1.enc} Output written on cyverse-foss.pdf (175 pages, 10786674 bytes). Transcript written on cyverse-foss.log. Latexmk: Index file 'cyverse-foss.idx' was written Latexmk: Missing input file: '{../img/cyverse_learning}.png' from line 'LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.' Latexmk: Missing input file: '{reproducible_science/./img/intercom}.png' from line 'LaTeX Warning: File `{reproducible_science/./img/intercom}.png' not found on in' Latexmk: Missing input file: '{reproducible_science/./img/intercom}.png' from line 'LaTeX Warning: File `{reproducible_science/./img/intercom}.png' not found on input line 2833.' Latexmk: Missing input file: '{cloud_comput/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{cloud_comput/../img/notebook_terminal}.png' not found on ' Latexmk: Missing input file: '{cloud_comput/../img/notebook_terminal}.png' from line 'LaTeX Warning: File `{cloud_comput/../img/notebook_terminal}.png' not found on input line 6686.' Latexmk: Log file says output to 'cyverse-foss.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-foss.out' 'cyverse-foss.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-foss" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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[169] [170] Chapter 3. (./cyverse-foss.ind) [171 <./intercom.png>] (./cyverse-foss.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc}{/usr/share/texmf/fonts/enc/dvips/cm-super/cm-s uper-ts1.enc} Output written on cyverse-foss.pdf (175 pages, 10786674 bytes). Transcript written on cyverse-foss.log. Latexmk: Index file 'cyverse-foss.idx' was written Latexmk: Missing input file: '{../img/cyverse_learning}.png' from line 'LaTeX Warning: File `{../img/cyverse_learning}.png' not found on input line 2.' Latexmk: Missing input file: '{reproducible_science/./img/intercom}.png' from line 'LaTeX Warning: File `{reproducible_science/./img/intercom}.png' not found on in' Latexmk: Missing input file: '{reproducible_science/./img/intercom}.png' from line 'LaTeX Warning: File `{reproducible_science/./img/intercom}.png' not found on input line 2833.' 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Latexmk: Log file says output to 'cyverse-foss.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2021-01-29T18:09:58.729280Z, end-time: 2021-01-29T18:09:58.788217Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/./_build/latex/cyverse-foss.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/artifacts/foss-2021-spring/sphinx_pdf/cyverse-foss.pdf [rtd-command-info] start-time: 2021-01-29T18:09:58.904571Z, end-time: 2021-01-29T18:10:06.916475Z, duration: 8, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees-epub -D language=en . _build/epub 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 [epub]: targets for 49 source files that are out of date updating environment: 49 added, 0 changed, 0 removed reading sources... 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[100%] software_essentials/linux /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/envs/foss-2021-spring/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/foss-2021-spring/.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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:2: WARNING: Duplicate explicit target name: "docker hub". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockeradvanced.rst:417: WARNING: Unknown target name: "see here". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerhandson.rst:35: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:498: WARNING: Duplicate explicit target name: "dockerfile". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:554: WARNING: Duplicate explicit target name: "build the image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:591: WARNING: Duplicate explicit target name: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/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-foss/checkouts/foss-2021-spring/Containers/dockerintro.rst:471: WARNING: Duplicate target name, cannot be used as a unique reference: "run your image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/dockeronatmo.rst:10: WARNING: Title underline too short. Launching a Docker app on Atmosphere --------------------------------- cyverse_rst_defined_substitutions.txt:36: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Containers/introtocontainers.rst:179: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:9: WARNING: Title underline too short. **Accessing Data Store** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:47: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:52: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:136: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/data_store.rst:155: WARNING: Title underline too short. Additional Resources ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:10: WARNING: Title underline too short. **Discovery Environment** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:37: WARNING: Title level inconsistent: **Find an app by** `searching `_ """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:40: WARNING: Title level inconsistent: **Browse by operation** """""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:45: WARNING: Title level inconsistent: **Find apps by community** """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-analysis.rst:93: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:10: WARNING: Title underline too short. **Discovery Environment - Data Management** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:16: WARNING: Title underline too short. DE Basics Walkthrough =============== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:54: WARNING: Title underline too short. Advanced Metadata Usage ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:80: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/de-data-manage.rst:100: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:188: WARNING: Title underline too short. `SciApps `_ ^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/intro_to_cyverse.rst:219: WARNING: Title underline too short. `The CyVerse Learning Center `_ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:8: WARNING: Title underline too short. **Discovery Environment - Tools & Apps** ===================================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:83: WARNING: Missing matching underline for section title overline. ---- .. Comment: Place URLS Below This Line /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/tool_integration_app_building_DE.rst:120: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:10: WARNING: Title underline too short. **Discovery Environment - VICE** ======== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/vice.rst:173: WARNING: At least one body element must separate transitions; adjacent transitions are not allowed. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:10: WARNING: Title underline too short. **Creating Workflows** ------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/CyVerse/workflow.rst:12: WARNING: Explicit markup ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:100: WARNING: Title underline too short. Hands on Exercise - Metadata in CyVerse ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:104: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:106: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:109: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/FAIR.rst:24: WARNING: Unknown target name: "fair guiding principles". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:9: WARNING: Title underline too short. **Data Management Plans (DMP)** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:30: WARNING: Title underline too short. Elements of a good DMP ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmp.rst:82: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/dmtools.rst:9: WARNING: Title underline too short. **Data Management Tools** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:9: WARNING: Title underline too short. **Data Management Overview** ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:14: WARNING: Title underline too short. Why should you care about data management? ============================ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:30: WARNING: Title underline too short. Data Management Basics =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:58: WARNING: Title underline too short. Best practices for the data life cycle ~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:84: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/Data_management/overview.rst:169: WARNING: Title underline too short. References and Resources ================= /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:58: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/installation.rst:50: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 2 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Tool/Software - Notes - Link * - A Second Monitor (highly recommended) - Having two monitors enables you to full-screen stream the instructional portion of the course while working on a second screen. This is particularly helpful if you currently only have a laptop screen. - * - SSH Clients (Windows) - PuTTY allows SSH connection to a remote machine, and is designed for Windows users who do not have a Mac/Linux terminal. MobaXterm is a single Windows application that provides a ton of functions for programmers, webmasters, IT administrators, and anybody is looking to manage system remotely - - `Download PuTTY `_ - `Download mobaXterm `_ - `Install Windows Subsystem for Linux (WSL) 2 `_ * - Text Editors - There is no 'best' text editor, but some are easier to use than others. Do some reading and pick one. - - `Atom `_ - `SublimeText `_ - `VisualStudioCode `_ - `Vim `_ - `Emacs `_ - `Nano `_ * - Cyberduck - Cyberduck is a third-party tool for uploading/downloading data to the CyVerse Data Store. Currently, this tool is available for Windows/MacOS only. You will need to download Cyberduck and the connection profile. We will go through configuration and installation during FOSS Onboarding. - - `Download Cyberduck `_ - `Installation for CyVerse `_ * - iCommands - iCommands are third-party software for command-line connection to the CyVerse Data Store. - Download and installation instructions available at `CyVerse Learning Center `__ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/before/main.rst:9: WARNING: Title underline too short. **Before FOSS Starts** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:21: WARNING: Title underline too short. **Virtual Machines on Atmosphere or Jetstream** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:65: WARNING: The "list-table" directive is empty; content required. .. list-table:: :header-rows: 1 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:9: WARNING: Duplicate explicit target name: "image". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:110: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:418: WARNING: Title underline too short. **Hands On** ------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:518: WARNING: Duplicate substitution definition name: "CyVerse_logo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:522: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:408: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/atmo.rst:511: WARNING: image file not readable: cloud_comput/../img/notebook_terminal.png /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:9: WARNING: Title underline too short. **Other Cyberinfrastructure Projects** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:12: WARNING: Title underline too short. **National Groups** ---------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:25: WARNING: Title underline too short. **Domain Specific Cyberinfrastructures** ------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:39: WARNING: Title underline too short. **Funding Opportunities** ----------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:42: WARNING: Title underline too short. **National Science Foundation** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:51: WARNING: Title underline too short. **National Institutes of Health** ~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:58: WARNING: Title underline too short. **Other US Federal** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:67: WARNING: Title underline too short. **Foundations** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/cyberinfrastructure.rst:76: WARNING: Title underline too short. **Big 3** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/intro.rst:10: WARNING: Title underline too short. **Introduction to Cloud Computing** =================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:10: WARNING: Title underline too short. **Research Cyberinfrastructure associated with CyVerse** ========================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:17: WARNING: Title underline too short. **XSEDE** -------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:30: WARNING: Title underline too short. **Jetstream** ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:39: WARNING: Title underline too short. **TACC** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:44: WARNING: Title underline too short. **Open Science Grid** ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/cloud_comput/xsede.rst:49: WARNING: Title underline too short. **CyVerse Powered By** ------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/colab_culture.rst:10: WARNING: Title underline too short. **Collaboration Culture and Roles** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:9: WARNING: Title underline too short. **Glossary & Acronyms** ^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/glossary.rst:47: WARNING: Inline emphasis start-string without end-string. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/instructors.rst:36: WARNING: Title underline too short. **CyVerse Staff** --------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:9: WARNING: Title underline too short. **About FOSS** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:24: WARNING: Title underline too short. **Learning Objectives** ==================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/intro.rst:41: WARNING: Title underline too short. **Approach** ~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/location.rst:9: WARNING: Title underline too short. **Location** ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:10: WARNING: Title underline too short. **Open Science Introductory Activity** ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/open_sci_lab.rst:22: WARNING: Title underline too short. **Planning your own Open Science lab** """""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:9: WARNING: Title underline too short. **Schedule** ========== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:82: WARNING: Title underline too short. Week 3: Feb. 23, 24 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:141: WARNING: Error parsing content block for the "list-table" directive: uniform two-level bullet list expected, but row 3 does not contain the same number of items as row 1 (2 vs 4). .. list-table:: :header-rows: 1 * - Time - Activity (Instructor) - Content - Expected Outcomes * - 0:00 - `Data Management Overview <../Data_management/overview.html>`_ - Organization, Sharing, Metadata - Understand why you need data management * - Guest Lecturer - Semantics, Ontologies, Metadata * - - `Data Management Tools <../Data_management/dmtools.html>`_ (Walls) - Open Science Framework, Protocols.io, CyVerse DataCommons - Creating data management plans, work with metadata * - - Homework for Week 5: `Data Management Plans <../Data_management/dmp.html>`_ (Walls) - Writing a Data Management Plan - Learn how to write an excellent DMP! /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:193: WARNING: Title underline too short. Week 7: Mar. 30, 31 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:246: WARNING: Title underline too short. Week 9: Apr. 13, 14 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/getting_started/schedule.rst:272: WARNING: Title underline too short. Week 10: Apr. 20, 21 ^^^^^^^^^^^^^^^^^^ cyverse_rst_defined_substitutions.txt:3: WARNING: Duplicate substitution definition name: "CyVerse User Portal". cyverse_rst_defined_substitutions.txt:7: WARNING: Duplicate substitution definition name: "Data Store". cyverse_rst_defined_substitutions.txt:11: WARNING: Duplicate substitution definition name: "Data Store Manual". cyverse_rst_defined_substitutions.txt:15: WARNING: Duplicate substitution definition name: "Data Store Guide". cyverse_rst_defined_substitutions.txt:19: WARNING: Duplicate substitution definition name: "Discovery Environment". cyverse_rst_defined_substitutions.txt:23: WARNING: Duplicate substitution definition name: "DE Manual". cyverse_rst_defined_substitutions.txt:27: WARNING: Duplicate substitution definition name: "Discovery Environment Guide". cyverse_rst_defined_substitutions.txt:31: WARNING: Duplicate substitution definition name: "Atmosphere". cyverse_rst_defined_substitutions.txt:35: WARNING: Duplicate substitution definition name: "Atmosphere Manual". cyverse_rst_defined_substitutions.txt:39: WARNING: Duplicate substitution definition name: "Atmosphere Guide". cyverse_rst_defined_substitutions.txt:43: WARNING: Duplicate substitution definition name: "BisQue". cyverse_rst_defined_substitutions.txt:47: WARNING: Duplicate substitution definition name: "BisQue Manual". cyverse_rst_defined_substitutions.txt:51: WARNING: Duplicate substitution definition name: "BisQue Guide". cyverse_rst_defined_substitutions.txt:55: WARNING: Duplicate substitution definition name: "DNA Subway". cyverse_rst_defined_substitutions.txt:59: WARNING: Duplicate substitution definition name: "DNA Subway Manual". cyverse_rst_defined_substitutions.txt:63: WARNING: Duplicate substitution definition name: "DNA Subway Guide". cyverse_rst_defined_substitutions.txt:67: WARNING: Duplicate substitution definition name: "Agave API". cyverse_rst_defined_substitutions.txt:71: WARNING: Duplicate substitution definition name: "Agave Live Docs". cyverse_rst_defined_substitutions.txt:75: WARNING: Duplicate substitution definition name: "Agave Guide". cyverse_rst_defined_substitutions.txt:79: WARNING: Duplicate substitution definition name: "SciApps". cyverse_rst_defined_substitutions.txt:83: WARNING: Duplicate substitution definition name: "SciApps Manual". cyverse_rst_defined_substitutions.txt:87: WARNING: Duplicate substitution definition name: "SciApps Guide". cyverse_rst_defined_substitutions.txt:91: WARNING: Duplicate substitution definition name: "Ask CyVerse". cyverse_rst_defined_substitutions.txt:95: WARNING: Duplicate substitution definition name: "CyVerse Learning Center". cyverse_rst_defined_substitutions.txt:99: WARNING: Duplicate substitution definition name: "CyVerse Wiki". cyverse_rst_defined_substitutions.txt:106: WARNING: Duplicate substitution definition name: "CyVerse_logo". cyverse_rst_defined_substitutions.txt:110: WARNING: Duplicate substitution definition name: "CyVerse_logo2". cyverse_rst_defined_substitutions.txt:114: WARNING: Duplicate substitution definition name: "Home_Icon". cyverse_rst_defined_substitutions.txt:118: WARNING: Duplicate substitution definition name: "Home_Icon2". cyverse_rst_defined_substitutions.txt:122: WARNING: Duplicate substitution definition name: "Intercom". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:10: WARNING: Title underline too short. Foundations of Open Science Skills 2021 ------------------------------------ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:182: WARNING: Duplicate substitution definition name: "CyVerse_logo2". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/index.rst:187: WARNING: Duplicate substitution definition name: "Home_Icon". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/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 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:34: WARNING: Unknown directive type "Goals". .. Goals:: - Feel comfortable using the GitHub environment - Integrate at least one repository onto GitHub /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:40: WARNING: Unknown directive type "Prerequisites". .. Prerequisites:: In order to complete this exercise you should have already installed ``git`` for the command line (`instructions `_) & created an account on the `GitHub `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:192: WARNING: Unknown directive type "Exercise". .. Exercise:: Create a new issue and relate it back to the issue you just created. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:349: WARNING: Unknown directive type "Definitions". .. Definitions:: **Git** - tool for version control. **GitHub** - hosted server that is also interactive. **repo** - short for repository; GitHub lets you create a remote repository online. **local** - on your personal computer. **clone** - copy of a repository that lives locally on your computer. Pushing changes will affect the repository online. **fetch** - getting latest changes to the repository on your local computer. **branch** - parallel to the master branch; allows you to make changes without affecting the master branch. Changes made on a branch can be merged back to the master. **fork** - copy of someone else's repository stored locally on your account. From forks, you can make pull requests to the master branch. **upstream** - primary or master branch of original repository. **downstream** - branch or fork of repository. **untracked** - changes made locally but not yet commited or pushed to the online repo. **staged** - item added to the repo. **commit** - finalize a change. **push** - add changes back to the remote repository. **merge** - takes changes from a branch or fork and applies them to the master. **pull request** - proposed changes to/within a repository. **issue** - suggestions or tasks needed for the repository. Allows you to track decisions, bugs with the repository, etc. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:432: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/GitHub.rst:410: WARNING: Error parsing content block for the "list-table" directive: two-level bullet list expected, but row 7 does not contain a second-level bullet list. .. list-table:: :header-rows: 1 * - Basic Snapshots - Command - Description * - - ``git status`` - Check status of the repository * - - ``git add [file-name.txt]`` - Add a file to "the staging area" * - - ``git add -A`` - Add all new and changed files to "the staging area" * - - ``git commit -m "[brief commit message]"`` - Commit changes to "the staging area" * - - ``git rm -r [file-name.txt]`` - Remove a file (or folder) * - -`git push` - Push changes to remote repository (remembered branch) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Title underline too short. **CI/CD** ====== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:30: WARNING: Title underline too short. **Continuous Development** ~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:44: WARNING: Title underline too short. **Waterfall** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:54: WARNING: Title underline too short. **Continuous Integration** ~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:71: WARNING: Title underline too short. **When to use CI?** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:78: WARNING: Title underline too short. **Travis CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:83: WARNING: Title underline too short. **Circle CI** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:88: WARNING: Title underline too short. **Jenkins** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:9: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:95: WARNING: Title underline too short. **GitHub Actions** """"""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:100: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:107: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:106: WARNING: Title level inconsistent: *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/cicd.rst:135: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:22: WARNING: Unknown directive type "remember". .. remember:: **SLACK** - Slack has `plenty of apps `_ for coordinating multiple services, i.e. Calendars, Github, GoogleDrive, Box, etc. - Slack is limiting unless you're willing to pay for the professional support. **Microsoft Teams** - Teams is used by many R1 research universities as part of their campus wide license agreement for Office 365 Business and Education. **Gitter** - Native integration with Github or Gitlab - Uses your GitHub username or Twitter handle for all Gitters you're a part of /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:39: WARNING: Title underline too short. *Other popular alternatives* """""""""""""""""""""""""" /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:53: WARNING: Title underline too short. *Create a SLACK Workspace* ~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:61: WARNING: Title underline too short. *Create a Gitter* ~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:66: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/communication.rst:77: WARNING: Title underline too short. **External** ---------- cyverse_rst_defined_substitutions.txt:122: WARNING: image file not readable: reproducible_science/./img/intercom.png cyverse_rst_defined_substitutions.txt:102: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:24: WARNING: Title underline too short. *Some things to remember* ---------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:27: WARNING: Title underline too short. *ReadTheDocs* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:34: WARNING: Title underline too short. *Bookdown* ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:9: WARNING: Duplicate explicit target name: "github pages". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:40: WARNING: Title underline too short. *GitHub Pages* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:46: WARNING: Title underline too short. *Confluence Wiki* ~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:91: WARNING: Title underline too short. *CyVerse Confluence Wiki* ~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/reproducible_science/websites.rst:100: WARNING: Title underline too short. **Methodology** ---------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:36: WARNING: Title underline too short. *R Markdown* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:44: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 3 supplied. .. code:: R ```{R, echo=FALSE} ``` ```{bash, echo=FALSE} ``` ```{python, echo=FALSE} ``` 4. Run the code block /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:57: WARNING: Title underline too short. *Workflow R* ~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:65: WARNING: Error in "code" directive: maximum 1 argument(s) allowed, 2 supplied. .. code:: install.package(c("workflowr","drake"), dependencies=TRUE) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:86: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "CyverseLogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Undefined substitution referenced: "LearningCenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "cyverselogo". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/RStudio_Git.rst:78: WARNING: Unknown target name: "learningcenter". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:26: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R setwd(path) getwd() #see what working directory you're in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:35: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:39: WARNING: Block quote ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:117: WARNING: Unexpected indentation. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:176: WARNING: Unknown directive type "code-blocl". .. code-blocl:: R #both do the same thing: require("package") #loads dependencies; will give a warning if it is in conflict with another package (e.g., masks) #can overwrite masked functions using "::" (e.g., package::function) library("package") #will give an error if in conflict with other packages or has missing dependencies /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:214: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.character() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:220: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.numeric() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:226: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 2 supplied. .. code-block:: R as.integer() /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:231: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R as.factor() #creates groupings within dataset /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:306: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 6 supplied. .. code-block:: R d <- c(d, "a) str(d) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:334: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hi <- data.frame(numbers = 1:26, letters, c("hey", "you")) /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:340: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 9 supplied. .. code-block:: R hola <- data.frame(1:26, letters, words = "hey", "you") /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:360: WARNING: Unknown directive type "code-black". .. code-black:: R hello[1:5, 2] hello$letters[1:5] /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:451: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 8 supplied. .. code-block:: R p <- subset(cats, cats$weight <= 3) p q <- cats[cats$weight <= 3,] q cats$likes_string == 1 cats[cats$likes_string == TRUE,] cats[c(1,3),] cats[colnames(cats) == "weight"] cats[cats$weight >= 2 & cats$weight <= 5] cats[cats$likes_string != 0,] #not equal to cats[!(is.na(cats$weight))] #is not /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:490: WARNING: Missing matching underline for section title overline. -------------- **Fix or improve this documentation:** - On Github: |Github Repo Link| /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:494: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Error in "image" directive: no content permitted. image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:496: WARNING: Substitution definition "R Console" empty or invalid. .. |R Console| image:: ../img/rstudio.png :width: 750 .. |Github Repo Link| raw:: html Github Repo Link /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/R_Studio.rst:55: WARNING: Undefined substitution referenced: "R Console". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:210: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 33 supplied. .. code-block:: bash $ ls -l total 576 drwxr-xr-x 7 amcooksey iplant-everyone 4096 Aug 7 20:14 data-shell -rw-r--r-- 1 amcooksey iplant-everyone 580102 Jan 29 10:54 data-shell.zip -rwxr-xr-x 1 amcooksey root 201 Jan 29 10:02 kanki.desktop /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:217: WARNING: Error in "code-block" directive: maximum 1 argument(s) allowed, 81 supplied. .. code-block:: bash $ cd data-shell $ ls -l total 52 drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 21:51 creatures drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 data drwxr-xr-x 2 amcooksey iplant-everyone 4096 Aug 7 20:13 molecules drwxr-xr-x 3 amcooksey iplant-everyone 4096 Aug 7 20:13 north-pacific-gyre -rw-r--r-- 1 amcooksey iplant-everyone 86 Aug 7 20:13 notes.txt -rw-r--r-- 1 amcooksey iplant-everyone 32 Aug 7 20:13 pizza.cfg -rw-r--r-- 1 amcooksey iplant-everyone 21583 Aug 7 20:13 solar.pdf drwxr-xr-x 5 amcooksey iplant-everyone 4096 Aug 7 20:14 writing /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:743: WARNING: Missing matching underline for section title overline. ------------- **Fix or improve this documentation:** /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:748: WARNING: Bullet list ends without a blank line; unexpected unindent. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:681: WARNING: Undefined substitution referenced: "nano>>". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:746: WARNING: Undefined substitution referenced: "Github Repo Link". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/commandline.rst:622: WARNING: Document may not end with a transition. /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Title underline too short. **Continuous Integration** ====================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:29: WARNING: Title underline too short. **Travis CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:34: WARNING: Title underline too short. **Circle CI** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:39: WARNING: Title underline too short. **Jenkins** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:10: WARNING: Duplicate explicit target name: "setup". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:46: WARNING: Title underline too short. **GitHub Actions** ~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:52: WARNING: Title underline too short. **Badges** ~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:59: WARNING: Title underline too short. *Different Badge Styles* --------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/continuous_integration.rst:87: WARNING: Title underline too short. **Self paced** ~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Title underline too short. **Basics of Linux** ================== /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:18: WARNING: Title underline too short. *Common Linux Operating Systems* -------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:32: WARNING: Title underline too short. *Installing Linux* ----------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:35: WARNING: Title underline too short. *Desktop-based Distributions* ~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "debian". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:43: WARNING: Title underline too short. *Windows Subsystem for Linux* ~~~~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:48: WARNING: Title underline too short. *Windows Linux Dual boot* ~~~~~~~~~~~~~~~~~~~~~~~~ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "ubuntu". /home/docs/checkouts/readthedocs.org/user_builds/cyverse-foss/checkouts/foss-2021-spring/software_essentials/linux.rst:9: WARNING: Duplicate explicit target name: "mint". 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