Read the Docs build information
Build id: 1662210
Project: northeastern-university-rc-public-documentation
Version: 127
Commit: 1a4d0f93c743396ac9ab376dc98981c757fa6ed9
Date: 2023-08-15T20:56:07.217652Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-08-15T20:56:16.831249Z, end-time: 2023-08-15T20:56:21.997603Z, duration: 5, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/northeastern-rc/rc-public-documentation .
Cloning into '.'...

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git fetch origin --force --tags --prune --prune-tags --depth 50 pull/127/head:external-127
From https://github.com/northeastern-rc/rc-public-documentation
 * [new ref]         refs/pull/127/head -> external-127

[rtd-command-info] start-time: 2023-08-15T20:56:23.563570Z, end-time: 2023-08-15T20:56:24.286696Z, duration: 0, exit-code: 0
git checkout --force 1a4d0f93c743396ac9ab376dc98981c757fa6ed9
Note: switching to '1a4d0f93c743396ac9ab376dc98981c757fa6ed9'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at 1a4d0f9 added R to the index

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git clean -d -f -f


[rtd-command-info] start-time: 2023-08-15T20:56:28.855679Z, end-time: 2023-08-15T20:56:33.754225Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/127/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/127/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2023-08-15T20:56:34.361960Z, end-time: 2023-08-15T20:56:35.577383Z, duration: 1, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/127/lib/python3.7/site-packages (23.2.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/envs/127/lib/python3.7/site-packages (68.0.0)

[rtd-command-info] start-time: 2023-08-15T20:56:36.006154Z, end-time: 2023-08-15T20:56:43.336316Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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Building wheels for collected packages: mock
  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=23753 sha256=06954d32ce8a4dc29d44d6a27c1bf0785701677756282e50aa9e1885b3ed8452
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Successfully built mock
Installing collected packages: snowballstemmer, pytz, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-9.5.0 pytz-2023.3 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.4

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python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
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[rtd-command-info] start-time: 2023-08-15T20:57:09.599659Z, end-time: 2023-08-15T20:57:09.662271Z, duration: 0, exit-code: 0
cat docs/source/conf.py
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
# list see the documentation:
# http://www.sphinx-doc.org/en/master/config

# -- Path setup --------------------------------------------------------------

# If extensions (or modules to document with autodoc) are in another directory,
# add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here.
#
# import os
# import sys
from datetime import date

# sys.path.insert(0, os.path.abspath('.'))


# -- Project information -----------------------------------------------------

project = "RC-HPC"
# logo = "_static/logo-square.png"
copyright = f"{date.today().year}, Andrey Petrov"
author = "Research Computing, NU"

# The full version, including alpha/beta/rc tags
release = "3.0.0"

# -- General configuration ---------------------------------------------------

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
    # "myst_nb",
    # Sphinx's own extensions
    "sphinx.ext.autodoc",
    "sphinx.ext.autosectionlabel",
    "sphinx.ext.extlinks",
    "sphinx.ext.intersphinx",
    "sphinx.ext.viewcode",
    "sphinx.ext.mathjax",
    "sphinx.ext.todo",
    "sphinx_copybutton",
    "sphinx_design",  # https://pypi.org/project/sphinx_design/
    # "sphinx_tabs.tabs",
    "sphinx_togglebutton",
    # https://sphinx-togglebutton.readthedocs.io/en/latest/use.html
    # "sphinxcontrib.bibtex",
    # "sphinxext.opengraph",
    # For the kitchen sink
    # Our custom extension, only meant for Furo's own documentation.
    "furo.sphinxext",
    # External stuff
    "myst_parser",
    "sphinx_copybutton",
    "sphinx_inline_tabs",
]

# Prefix document path to section labels, to use:
# `path/to/file:heading` instead of just `heading`
autosectionlabel_prefix_document = True

intersphinx_mapping = {"python": ("https://docs.python.org/3", None),
                       "sphinx": ("https://www.sphinx-doc.org/en/master", None)}

# -- Options for TODOs -------------------------------------------------------
#
todo_include_todos = True

# -- Options for Markdown files ----------------------------------------------
#

myst_enable_extensions = [
    "colon_fence",
    "deflist",
    "dollarmath",
]
myst_heading_anchors = 3
myst_deflist_enable = True
# Add any paths that contain templates here, relative to this directory.
templates_path = ["_templates"]

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
# This pattern also affects html_static_path and html_extra_path.
exclude_patterns = ["using-ood/cps_ood.md",
                    "_snippets/*"]

# -- Options for HTML output -------------------------------------------------

# The theme to use for HTML and HTML Help pages.  See the documentation for
# a list of builtin themes.
#
html_theme = "furo"
html_title = "RC RTD"

html_theme_options = {
    "footer_icons": [
        {
            "name": "GitHub",
            "url": "https://github.com/northeastern-rc/rc-public-documentation",
            "html": """
                <svg stroke="currentColor" fill="currentColor" stroke-width="0" viewBox="0 0 16 16">
                    <path fill-rule="evenodd" d="M8 0C3.58 0 0 3.58 0 8c0 3.54 2.29 6.53 5.47 7.59.4.07.55-.17.55-.38 0-.19-.01-.82-.01-1.49-2.01.37-2.53-.49-2.69-.94-.09-.23-.48-.94-.82-1.13-.28-.15-.68-.52-.01-.53.63-.01 1.08.58 1.23.82.72 1.21 1.87.87 2.33.66.07-.52.28-.87.51-1.07-1.78-.2-3.64-.89-3.64-3.95 0-.87.31-1.59.82-2.15-.08-.2-.36-1.02.08-2.12 0 0 .67-.21 2.2.82.64-.18 1.32-.27 2-.27.68 0 1.36.09 2 .27 1.53-1.04 2.2-.82 2.2-.82.44 1.1.16 1.92.08 2.12.51.56.82 1.27.82 2.15 0 3.07-1.87 3.75-3.65 3.95.29.25.54.73.54 1.48 0 1.07-.01 1.93-.01 2.2 0 .21.15.46.55.38A8.013 8.013 0 0 0 16 8c0-4.42-3.58-8-8-8z"></path>
                </svg>
            """,
            "class": "",
        },
    ],
    # "announcement": """
    # <a style=\"text-decoration: none; color: white;\"
    #    href=\"https://github.com/sponsors/urllib3\">
    #    <img src=\"_static/image/logo-square.png\"/> Submit a ticket for support
    # </a>
    # """,
    "sidebar_hide_name": True,
    # add logo to the upper left in the help system
    "light_logo": "image/nu-logo-light.png",
    "dark_logo": "image/nu-logo-dark.png",
}

# custom css file
html_css_files = ["../css/custom.css"]

# If true, “(C) Copyright …” is shown in the HTML footer. Default is True.
html_show_copyright = True
# If true, “Created using Sphinx” is shown in the HTML footer. Default is True.
html_show_sphinx = False

# Add any paths that contain custom static files (such as style sheets) here,
# relative to this directory. They are copied after the builtin static files,
# so a file named "default.css" will overwrite the builtin "default.css".
html_static_path = ["_static", "_static/video"]

master_doc = "index"
source_suffix = [".rst", ".md"]

# Warn about all references to unknown targets
nitpicky = True




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

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

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes
        SUFFIX = list(source_suffix.keys())[0]  # make a ``list()`` for py2/py3 compatibility
    else:
        # default to .rst
        SUFFIX = '.rst'
else:
    SUFFIX = '.rst'

# Add RTD Static Path. Add to the end because it overwrites previous files.
if not 'html_static_path' in globals():
    html_static_path = []
if os.path.exists('_static'):
    html_static_path.append('_static')

# Add RTD Theme only if they aren't overriding it already
using_rtd_theme = (
    (
        'html_theme' in globals() and
        html_theme in ['default'] and
        # Allow people to bail with a hack of having an html_style
        'html_style' not in globals()
    ) or 'html_theme' not in globals()
)
if using_rtd_theme:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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': "127",
    'version_slug': "127",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("2.0.0", "/en/2.0.0/"),
    ("1.2.0", "/en/1.2.0/"),
    ("v1.1.0", "/en/v1.1.0/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'northeastern-university-rc-public-documentation',
    'name': u'rc-public-documentation',
    'rtd_language': u'en',
    'programming_language': u'words',
    'canonical_url': '',
    'analytics_code': 'UA-53190950-13',
    'single_version': False,
    'conf_py_path': '/docs/source/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'northeastern-rc',
    'proxied_api_host': '/_',
    'github_repo': 'rc-public-documentation',
    'github_version': '1a4d0f93c743396ac9ab376dc98981c757fa6ed9',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '1a4d0f93c743396ac9ab376dc98981c757fa6ed9',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '1a4d0f93c743396ac9ab376dc98981c757fa6ed9',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': 'UA-53190950-13',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '1a4d0f93',
}

# 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():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
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 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/northeastern-rc/rc-public-documentation/pull/127'
    readthedocs_build_url = 'https://readthedocs.com/projects/northeastern-university-rc-public-documentation/builds/1662210/'

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: 2023-08-15T20:57:10.152717Z, end-time: 2023-08-15T20:57:20.798067Z, duration: 10, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v5.3.0
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://www.sphinx-doc.org/en/master/objects.inv...
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist', 'dollarmath'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 80 source files that are out of date
updating environment: [new config] 80 added, 0 changed, 0 removed
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reading sources... [100%] welcome/welcome

/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/software/conda.md:7: WARNING: Document headings start at H2, not H1 [myst.header]
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/software/spack.md:2: WARNING: Document headings start at H2, not H1 [myst.header]
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/understandingsystem/usingbash.md:575: WARNING: download file not readable: /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/_resources/awk-example.txt
looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/feedback/reportbug.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/gettingsoftware/cmake.md: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/gettingsoftware/makefile.md: WARNING: document isn't included in any toctree
done
preparing documents... done
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writing output... [  2%] additionalresources/casestudiesandtestimonials
writing output... [  3%] additionalresources/communityandforums
writing output... [  5%] additionalresources/faq
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writing output... [  7%] additionalresources/index
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writing output... [ 20%] classroom/index
writing output... [ 21%] datamanagement/databackup
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/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/best-practices/homequota.md:97: WARNING: undefined label: 'using-conda'
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/best-practices/homequota.md:99: WARNING: undefined label: 'using-conda'
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/gettingsoftware/index.md:26: WARNING: term not in glossary: 'Package managers'
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/software/softwareoverview.md:24: WARNING: undefined label: 'using-spack'
/home/docs/checkouts/readthedocs.org/user_builds/northeastern-university-rc-public-documentation/checkouts/127/docs/source/software/softwareoverview.md:29: WARNING: undefined label: 'using-conda'
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copying static files... done
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dumping object inventory... done
Updating searchtools for Read the Docs search... build succeeded, 11 warnings.

The HTML pages are in ../../_readthedocs/html.