Read the Docs build information Build id: 920585 Project: beliveau-lab-tigerfish Version: latest Commit: 9fbb78472ed7e23ecf39dd1d2a2cb01292b67180 Date: 2022-04-19T02:47:04.436726Z State: finished Success: False [rtd-command-info] start-time: 2022-04-19T02:47:06.197309Z, end-time: 2022-04-19T02:47:08.432909Z, duration: 2, 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: 2022-04-19T02:47:08.623078Z, end-time: 2022-04-19T02:47:08.984492Z, 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 9fbb784 modify conf [rtd-command-info] start-time: 2022-04-19T02:47:09.159895Z, end-time: 2022-04-19T02:47:09.228521Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-04-19T02:47:10.377091Z, end-time: 2022-04-19T02:47:14.784323Z, 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: 2022-04-19T02:47:14.966086Z, end-time: 2022-04-19T02:47:16.839467Z, duration: 1, 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 33.9 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: 2022-04-19T02:47:17.013833Z, end-time: 2022-04-19T02:47:25.321187Z, 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 32.1 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 186.7 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 173.9 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 181.7 MB/s eta 0:00:00 Collecting sphinx-rtd-theme 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pyparsing!=3.0.5,>=2.0.2 Downloading pyparsing-3.0.8-py3-none-any.whl (98 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 98.5/98.5 KB 183.3 MB/s eta 0:00:00 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=75d9f201fb5a6ffadadef29f09b14c513f78ddef82327af9c45b689099b40449 Stored in directory: /tmp/pip-ephem-wheel-cache-g2ekw_w_/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=f7dbeb8b0fe400b4cf1f557dfd10a8c891c87e39b1d7220e9e2259b811360d4b Stored in directory: /tmp/pip-ephem-wheel-cache-g2ekw_w_/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: 2022-04-19T02:47:25.502611Z, end-time: 2022-04-19T02:47:44.003502Z, duration: 18, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[docs] Processing /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/checkouts/latest Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting numpy>=1.18.1 Downloading numpy-1.21.6-cp37-cp37m-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (15.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.7/15.7 MB 195.4 MB/s eta 0:00:00 Collecting pandas>=1.0.3 Downloading pandas-1.3.5-cp37-cp37m-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.3 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.3/11.3 MB 195.7 MB/s eta 0:00:00 Collecting biopython>=1.77 Downloading 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/tmp/pip-ephem-wheel-cache-podvysfh/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: 2022-04-19T02:47:45.398524Z, end-time: 2022-04-19T02:47:45.461824Z, 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: # https://www.sphinx-doc.org/en/master/usage/configuration.html # -- 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 import subprocess from configparser import RawConfigParser import sphinx_rtd_theme sys.path.insert(0, os.path.abspath(os.path.join("..", ".."))) try: import numpydoc except ModuleNotFoundError: subprocess.run(["pip", "install", "numpydoc"], check=True) # -- Project information ----------------------------------------------------- project = 'Tigerfish' copyright = '2022, Robin Aguilar' author = 'Robin Aguilar' # The full version, including alpha/beta/rc tags release = '2022' # -- General configuration --------------------------------------------------- #def get_version(): # """Return package version from setup.cfg.""" # config = RawConfigParser() # config.read(os.path.join('.', 'setup.cfg')) # return config.get('metadata', 'version') # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ "sphinx.ext.autodoc", "sphinx.ext.autosummary", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.viewcode", "numpydoc", "sphinx_rtd_theme", "sphinx.ext.intersphinx", "sphinxarg.ext", "nbsphinx", "recommonmark", "sphinx.ext.duration", "sphinx_tabs.tabs", "sphinx.ext.doctest", "sphinx-prompt", "sphinx_search.extension", "sphinx.ext.intersphinx", "sphinxemoji.sphinxemoji", "myst_parser", ] nbsphinx_execute = "never" autosummary_generate = True autodoc_default_options = { "members": True, "inherited-members": True, "member-order": "bysource", } numpydoc_show_class_members = True numpydoc_show_inherited_class_members = True numpydoc_attributes_as_param_list = True intersphinx_mapping = { "pandas": ("https://pandas.pydata.org/docs", None), "sklearn": ("https://scikit-learn.org/stable", None), "numpy": ("https://numpy.org/doc/stable", None), "matplotlib": ("https://matplotlib.org", None), } # Add any paths that contain templates here, relative to this directory. templates_path = ['_templates'] # The root document. root_doc = 'index.rst' # 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 = [] # -- 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 = 'sphinx_rtd_theme' master_doc = "index" source_suffix = [".rst", ".md"] html_theme_options = { "style_nav_header_background": "#343131", "logo_only": True, } html_css_files = [ "custom.css", ] # 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'] ########################################################################### # 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/source/', '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': '9fbb7847', } # 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/920585/' 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: 2022-04-19T02:47:45.740543Z, end-time: 2022-04-19T02:47:46.681872Z, 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 Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/registry.py", line 425, in load_extension mod = import_module(extname) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/importlib/__init__.py", line 127, in import_module return _bootstrap._gcd_import(name[level:], package, level) File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 953, in _find_and_load_unlocked File "", line 219, in _call_with_frames_removed File "", line 1006, in _gcd_import File "", line 983, in _find_and_load File "", line 965, in _find_and_load_unlocked ModuleNotFoundError: No module named 'sphinx_tabs' The above exception was the direct cause of the following exception: 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 275, in build_main args.tags, args.verbosity, args.jobs, args.keep_going) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 223, in __init__ self.setup_extension(extension) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/application.py", line 380, in setup_extension self.registry.load_extension(self, extname) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.7/site-packages/sphinx/registry.py", line 429, in load_extension err) from err sphinx.errors.ExtensionError: Could not import extension sphinx_tabs.tabs (exception: No module named 'sphinx_tabs') Extension error: Could not import extension sphinx_tabs.tabs (exception: No module named 'sphinx_tabs')