Read the Docs build information Build id: 921293 Project: beliveau-lab-tigerfish Version: latest Commit: 2d95e9d2029a90667c394a7236667ca0984dcc42 Date: 2022-04-19T16:47:38.931202Z State: finished Success: False [rtd-command-info] start-time: 2022-04-19T16:47:40.710927Z, end-time: 2022-04-19T16:47:45.871933Z, duration: 5, exit-code: 0 git clone --no-single-branch --depth 50 git@github.com:beliveau-lab/TigerFISH.git . Cloning into '.'... Warning: Permanently added 'github.com,192.30.255.112' (ECDSA) to the list of known hosts. [rtd-command-info] start-time: 2022-04-19T16:47:46.159188Z, end-time: 2022-04-19T16:47:46.515228Z, 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 Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at 2d95e9d updated conf [rtd-command-info] start-time: 2022-04-19T16:47:46.766712Z, end-time: 2022-04-19T16:47:46.837718Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-04-19T16:47:47.919778Z, end-time: 2022-04-19T16:47:52.433899Z, duration: 4, 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: 2022-04-19T16:47:52.663073Z, end-time: 2022-04-19T16:47:54.752108Z, 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) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 946.1/946.1 KB 28.6 MB/s eta 0:00:00 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: 2022-04-19T16:47:54.928465Z, end-time: 2022-04-19T16:48:03.380666Z, duration: 8, 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 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 KB 25.1 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.0/2.0 MB 183.8 MB/s eta 0:00:00 Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 47.4/47.4 KB 174.9 MB/s eta 0:00:00 Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx Downloading Sphinx-4.5.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 202.6 MB/s eta 0:00:00 Collecting sphinx-rtd-theme 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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 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/tmp/pip-ephem-wheel-cache-1hs6v7z4/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, 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: 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-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: 2022-04-19T16:48:23.402107Z, end-time: 2022-04-19T16:48:23.464023Z, 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': '2d95e9d2', } # 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/921293/' 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: 2022-04-19T16:48:23.636993Z, end-time: 2022-04-19T16:48:24.322743Z, 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: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