Read the Docs build information
Build id: 921223
Project: beliveau-lab-tigerfish
Version: latest
Commit: 2a5b15f9f94889ecddcb0f206938980d7be43763
Date: 2022-04-19T16:09:49.387850Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-04-19T16:15:34.732449Z, end-time: 2022-04-19T16:15:39.418805Z, duration: 4, exit-code: 0
git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git .
Cloning into '.'...
Warning: Permanently added 'github.com,192.30.255.113' (ECDSA) to the list of known hosts.

[rtd-command-info] start-time: 2022-04-19T16:15:39.609407Z, end-time: 2022-04-19T16:15:39.968271Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to 'origin/master'.

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

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

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

HEAD is now at 2a5b15f modify index

[rtd-command-info] start-time: 2022-04-19T16:15:40.143201Z, end-time: 2022-04-19T16:15:40.218777Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-04-19T16:15:41.514143Z, end-time: 2022-04-19T16:16:00.242269Z, duration: 18, 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/beliveau-lab-tigerfish/envs/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-04-19T16:16:00.429571Z, end-time: 2022-04-19T16:16:02.723085Z, duration: 2, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (22.0.4)
Collecting setuptools<58.3.0
  Downloading setuptools-58.2.0-py3-none-any.whl (946 kB)
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Installing collected packages: setuptools
  Attempting uninstall: setuptools
    Found existing installation: setuptools 62.1.0
    Uninstalling setuptools-62.1.0:
      Successfully uninstalled setuptools-62.1.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-04-19T16:16:02.903308Z, end-time: 2022-04-19T16:16:12.295707Z, duration: 9, exit-code: 0
python -m pip install --upgrade --no-cache-dir mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx sphinx-rtd-theme readthedocs-sphinx-ext<2.2
Collecting mock==1.0.1
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  Preparing metadata (setup.py): started
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Collecting pillow==5.4.1
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Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting sphinx
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Collecting readthedocs-sphinx-ext<2.2
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Collecting future
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Collecting docutils>=0.11
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Collecting sphinxcontrib-jsmath
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Collecting Jinja2>=2.3
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Collecting docutils>=0.11
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Collecting requests>=2.5.0
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Collecting imagesize
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Collecting sphinxcontrib-qthelp
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Collecting sphinxcontrib-applehelp
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Collecting snowballstemmer>=1.1
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Collecting babel>=1.3
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Collecting importlib-metadata>=4.4
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Collecting sphinxcontrib-serializinghtml>=1.1.5
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Collecting Pygments>=2.0
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Collecting packaging
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Collecting sphinxcontrib-htmlhelp>=2.0.0
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Collecting pytz>=2015.7
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Collecting typing-extensions>=3.6.4
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Collecting MarkupSafe>=2.0
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Collecting certifi>=2017.4.17
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Collecting idna<4,>=2.5
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Collecting urllib3<1.27,>=1.21.1
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Collecting charset-normalizer~=2.0.0
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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=23773 sha256=243df7335be78491069d99dc77281da2b5174dafc2d6d860fd8504c808f264d3
  Stored in directory: /tmp/pip-ephem-wheel-cache-jxqyem40/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=491070 sha256=07f6b5a1bd719c8d6e9d9d33657d73c077120541e5d51fe427757c70f127b196
  Stored in directory: /tmp/pip-ephem-wheel-cache-jxqyem40/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: snowballstemmer, pytz, mock, certifi, alabaster, zipp, urllib3, typing-extensions, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, babel, requests, packaging, Jinja2, importlib-metadata, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed Jinja2-3.1.1 MarkupSafe-2.1.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 importlib-metadata-4.11.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.8 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 snowballstemmer-2.2.0 sphinx-4.5.0 sphinx-rtd-theme-1.0.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 typing-extensions-4.2.0 urllib3-1.26.9 zipp-3.8.0

[rtd-command-info] start-time: 2022-04-19T16:16:12.479164Z, end-time: 2022-04-19T16:16:14.749140Z, duration: 2, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt
Collecting sphinx==3.4.3
  Downloading Sphinx-3.4.3-py3-none-any.whl (2.9 MB)
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Collecting sphinx_autodoc_typehints==1.12.0
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Collecting sphinx_autodoc_defaultargs==0.1.2
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Requirement already satisfied: sphinxcontrib-jsmath in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (1.0.1)
Requirement already satisfied: sphinxcontrib-htmlhelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (2.0.0)
Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (1.1.5)
Requirement already satisfied: sphinxcontrib-qthelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (1.0.3)
Requirement already satisfied: requests>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (2.27.1)
Requirement already satisfied: sphinxcontrib-devhelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (1.0.2)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (3.1.1)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (21.3)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (58.2.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (1.3.0)
Requirement already satisfied: babel>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (2.9.1)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (0.7.12)
Requirement already satisfied: sphinxcontrib-applehelp in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (1.0.2)
Requirement already satisfied: docutils>=0.12 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (0.17.1)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (2.11.2)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from sphinx==3.4.3->-r docs/requirements.txt (line 1)) (2.2.0)
Requirement already satisfied: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages (from babel>=1.3->sphinx==3.4.3->-r docs/requirements.txt (line 1)) (2022.1)
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Collecting importlib-resources>=1.4.0
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Collecting attrs>=17.4.0
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Collecting ptyprocess>=0.5
  Downloading ptyprocess-0.7.0-py2.py3-none-any.whl (13 kB)
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  Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
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Collecting soupsieve>1.2
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Building wheels for collected packages: Tigerfish
  Building wheel for Tigerfish (setup.py): started
  Building wheel for Tigerfish (setup.py): finished with status 'done'
  Created wheel for Tigerfish: filename=Tigerfish-0.0.0-py3-none-any.whl size=3744 sha256=e0322959108931e131dffd39eb7f35f132f733d13dedc47ca0320b918912a2ea
  Stored in directory: /tmp/pip-ephem-wheel-cache-glz_7mpu/wheels/b0/9b/e1/5f4d486d1a19ff5976dc7facfcbe554798f1d49bfd6f969745
Successfully built Tigerfish
Installing collected packages: webencodings, wcwidth, ptyprocess, pickleshare, mistune, fastjsonschema, commonmark, backcall, traitlets, tornado, tinycss2, soupsieve, six, setuptools, pyzmq, pyrsistent, psutil, prompt-toolkit, pexpect, parso, pandocfilters, numpy, nest-asyncio, jupyterlab-pygments, jinja2, importlib-resources, entrypoints, defusedxml, decorator, debugpy, attrs, sphinx, python-dateutil, matplotlib-inline, jupyter-core, jsonschema, jedi, bleach, biopython, beautifulsoup4, sphinx-argparse, recommonmark, pandas, numpydoc, nbformat, jupyter-client, ipython, Tigerfish, nbclient, ipykernel, nbconvert, nbsphinx
  Attempting uninstall: commonmark
    Found existing installation: commonmark 0.8.1
    Uninstalling commonmark-0.8.1:
      Successfully uninstalled commonmark-0.8.1
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.2.0
    Uninstalling setuptools-58.2.0:
      Successfully uninstalled setuptools-58.2.0
  Attempting uninstall: jinja2
    Found existing installation: Jinja2 3.1.1
    Uninstalling Jinja2-3.1.1:
      Successfully uninstalled Jinja2-3.1.1
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 3.4.3
    Uninstalling Sphinx-3.4.3:
      Successfully uninstalled Sphinx-3.4.3
  Attempting uninstall: recommonmark
    Found existing installation: recommonmark 0.5.0
    Uninstalling recommonmark-0.5.0:
      Successfully uninstalled recommonmark-0.5.0
Successfully installed Tigerfish-0.0.0 attrs-21.4.0 backcall-0.2.0 beautifulsoup4-4.11.1 biopython-1.79 bleach-5.0.0 commonmark-0.9.1 debugpy-1.6.0 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 fastjsonschema-2.15.3 importlib-resources-5.7.1 ipykernel-6.13.0 ipython-7.32.0 jedi-0.18.1 jinja2-3.0.3 jsonschema-4.4.0 jupyter-client-7.2.2 jupyter-core-4.10.0 jupyterlab-pygments-0.2.2 matplotlib-inline-0.1.3 mistune-0.8.4 nbclient-0.6.0 nbconvert-6.5.0 nbformat-5.3.0 nbsphinx-0.8.8 nest-asyncio-1.5.5 numpy-1.21.6 numpydoc-1.2.1 pandas-1.3.5 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 prompt-toolkit-3.0.29 psutil-5.9.0 ptyprocess-0.7.0 pyrsistent-0.18.1 python-dateutil-2.8.2 pyzmq-22.3.0 recommonmark-0.7.1 setuptools-62.1.0 six-1.16.0 soupsieve-2.3.2.post1 sphinx-4.5.0 sphinx-argparse-0.3.1 tinycss2-1.1.1 tornado-6.1 traitlets-5.1.1 wcwidth-0.2.5 webencodings-0.5.1

[rtd-command-info] start-time: 2022-04-19T16:16:36.919187Z, end-time: 2022-04-19T16:16:36.996134Z, duration: 0, exit-code: 0
cat docs/conf.py
###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


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

import importlib
import sys
import os.path

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

from sphinx import version_info

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

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

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

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'beliveau-lab-tigerfish',
    'name': u'TigerFISH',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://beliveau-lab-tigerfish.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'beliveau-lab',
    'proxied_api_host': '/_',
    'github_repo': 'TigerFISH',
    'github_version': 'master',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'master',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'master',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '2a5b15f9',
}

# 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/beliveau-lab-tigerfish/builds/921223/'

project_language = 'en'

# User's Sphinx configurations
language_user = globals().get('language', None)
latex_engine_user = globals().get('latex_engine', None)
latex_elements_user = globals().get('latex_elements', None)

# Remove this once xindy gets installed in Docker image and XINDYOPS
# env variable is supported
# https://github.com/rtfd/readthedocs-docker-images/pull/98
latex_use_xindy = False

chinese = any([
    language_user in ('zh_CN', 'zh_TW'),
    project_language in ('zh_CN', 'zh_TW'),
])

japanese = any([
    language_user == 'ja',
    project_language == 'ja',
])

if chinese:
    latex_engine = latex_engine_user or 'xelatex'

    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
    }
    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

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

[rtd-command-info] start-time: 2022-04-19T16:16:37.214469Z, end-time: 2022-04-19T16:16:38.125746Z, duration: 0, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.5.0
loading translations [en]... done
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 1 source files that are out of date
updating environment: [new config] 1 added, 0 changed, 0 removed
reading sources... [100%] source/index

/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:7: WARNING: Title underline too short.

Tigerfish: A tool for repetitive DNA oligonucleotide probe design
=======================================
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:12: ERROR: Undefined substitution referenced: ":microscope:".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:15: ERROR: Undefined substitution referenced: ":bar_chart:".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:18: ERROR: Undefined substitution referenced: ":tropical_fish:".
/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/source/index.rst:20: ERROR: Undefined substitution referenced: ":fish:".

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/cmd/build.py", line 276, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 330, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 288, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 300, in build
    updated_docnames = set(self.read())
  File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 411, in read
    self.env.doc2path(self.config.root_doc))
sphinx.errors.SphinxError: root file /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/index.rst not found

Sphinx error:
root file /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest/docs/index.rst not found