Read the Docs build information Build id: 1953758 Project: beliveau-lab-tigerfish Version: latest Commit: 8685e8a3a8851a0cd9524c0c609cd7b9d167f650 Date: 2024-01-16T20:16:24.935582Z State: finished Success: False [rtd-command-info] start-time: 2024-01-16T20:16:26.049066Z, end-time: 2024-01-16T20:16:33.184795Z, duration: 7, exit-code: 0 git clone --depth 1 git@github.com:beliveau-lab/TigerFISH.git . Cloning into '.'... Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. [rtd-command-info] start-time: 2024-01-16T20:16:33.250236Z, end-time: 2024-01-16T20:16:41.939265Z, duration: 8, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. Warning: Permanently added 'github.com' (ED25519) to the list of known hosts. From github.com:beliveau-lab/TigerFISH * [new tag] v1.1.0 -> v1.1.0 [rtd-command-info] start-time: 2024-01-16T20:16:42.061301Z, end-time: 2024-01-16T20:16:42.568437Z, 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 8685e8a Update snakemake_env.yml [rtd-command-info] start-time: 2024-01-16T20:16:42.639811Z, end-time: 2024-01-16T20:16:42.699418Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-01-16T20:16:42.782525Z, end-time: 2024-01-16T20:16:42.835518Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: "ubuntu-22.04" tools: python: "3.11" sphinx: configuration: docs/source/conf.py python: install: - requirements: docs/requirements.txt [rtd-command-info] start-time: 2024-01-16T20:16:49.870901Z, end-time: 2024-01-16T20:16:49.952751Z, duration: 0, exit-code: 0 asdf global python 3.11.6 [rtd-command-info] start-time: 2024-01-16T20:16:50.400828Z, end-time: 2024-01-16T20:16:51.534620Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.6.final.0-64 in 815ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest, clear=False, no_vcs_ignore=False, global=False) seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv) added seed packages: pip==23.1, setuptools==67.6.1, wheel==0.40.0 activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2024-01-16T20:16:51.602746Z, end-time: 2024-01-16T20:17:02.052461Z, duration: 10, 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/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (23.1) Collecting pip Downloading pip-23.3.2-py3-none-any.whl (2.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 8.4 MB/s eta 0:00:00 Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages (67.6.1) Collecting setuptools Downloading setuptools-69.0.3-py3-none-any.whl (819 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 819.5/819.5 kB 20.9 MB/s eta 0:00:00 Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 67.6.1 Uninstalling setuptools-67.6.1: Successfully uninstalled setuptools-67.6.1 Attempting uninstall: pip Found existing installation: pip 23.1 Uninstalling pip-23.1: Successfully uninstalled pip-23.1 Successfully installed pip-23.3.2 setuptools-69.0.3 [rtd-command-info] start-time: 2024-01-16T20:17:02.122192Z, end-time: 2024-01-16T20:17:08.135385Z, duration: 6, exit-code: 0 python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext Collecting sphinx Downloading sphinx-7.2.6-py3-none-any.whl.metadata (5.9 kB) Collecting 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(104 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 104.6/104.6 kB 293.2 MB/s eta 0:00:00 Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx, readthedocs-sphinx-ext Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.3 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2023.11.17 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.1.0 [rtd-command-info] start-time: 2024-01-16T20:17:08.211537Z, end-time: 2024-01-16T20:17:15.607401Z, duration: 7, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r docs/requirements.txt Collecting Sphinx==4.4.0 (from -r docs/requirements.txt (line 3)) Downloading Sphinx-4.4.0-py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 15.5 MB/s eta 0:00:00 Collecting Pygments==2.11.2 (from -r docs/requirements.txt (line 4)) Downloading Pygments-2.11.2-py3-none-any.whl (1.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.1/1.1 MB 29.8 MB/s eta 0:00:00 Collecting sphinx_rtd_theme==1.0.0 (from -r docs/requirements.txt (line 6)) Downloading sphinx_rtd_theme-1.0.0-py2.py3-none-any.whl (2.8 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.8/2.8 MB 42.5 MB/s eta 0:00:00 Collecting sphinx-tabs==3.2.0 (from -r docs/requirements.txt (line 7)) Downloading sphinx_tabs-3.2.0-py3-none-any.whl (9.8 kB) Collecting sphinx-intl==2.0.1 (from -r docs/requirements.txt (line 8)) Downloading sphinx-intl-2.0.1.tar.gz (17 kB) Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting readthedocs-sphinx-search==0.1.1 (from -r docs/requirements.txt (line 10)) Downloading readthedocs_sphinx_search-0.1.1-py3-none-any.whl (18 kB) Collecting sphinxemoji==0.2.0 (from -r docs/requirements.txt (line 13)) Downloading sphinxemoji-0.2.0.tar.gz (44 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 44.4/44.4 kB 222.8 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' Collecting sphinxcontrib-httpdomain==1.8.0 (from -r docs/requirements.txt (line 14)) Downloading sphinxcontrib_httpdomain-1.8.0-py2.py3-none-any.whl (19 kB) Collecting sphinx-prompt==1.4.0 (from -r docs/requirements.txt (line 15)) Downloading sphinx_prompt-1.4.0-py3-none-any.whl (4.1 kB) Collecting sphinx-notfound-page==0.8 (from -r docs/requirements.txt (line 16)) Downloading sphinx_notfound_page-0.8-py3-none-any.whl (15 kB) Collecting sphinx-autobuild==2021.3.14 (from 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sha256=0505d28da5339474cc660d2eef0c18ac90b04e62e03fa49588306d89cab8a740 Stored in directory: /tmp/pip-ephem-wheel-cache-ueya6a0f/wheels/17/4c/42/ed7529920684c8534a0c2541942f1c70fd1baa7fdd02918321 Building wheel for sphinxemoji (setup.py): started Building wheel for sphinxemoji (setup.py): finished with status 'done' Created wheel for sphinxemoji: filename=sphinxemoji-0.2.0-py3-none-any.whl size=44408 sha256=a45bb40baa5f6554e5227e1b4ba11517396a2f6243d3c785c1a02de0e9228dd0 Stored in directory: /tmp/pip-ephem-wheel-cache-ueya6a0f/wheels/d4/b0/a5/92b0e0b5611fc4d37f90711172a680959318c4474df5d2718d Building wheel for rstcheck (setup.py): started Building wheel for rstcheck (setup.py): finished with status 'done' Created wheel for rstcheck: filename=rstcheck-3.3.1-py3-none-any.whl size=13717 sha256=3736d1b2d9a179588622e4b4b61f186c0b45c4d2598de0a56536e2bca511800a Stored in directory: /tmp/pip-ephem-wheel-cache-ueya6a0f/wheels/e0/57/d7/2af930ae6114f46c59f8f9807d39657196c217e4af0c4a9435 Successfully built sphinx-intl sphinxemoji rstcheck Installing collected packages: sphinx-notfound-page, tornado, six, readthedocs-sphinx-search, pyyaml, Pygments, mdurl, docutils, colorama, click, Sphinx, rstcheck, markdown-it-py, livereload, sphinxemoji, sphinxcontrib-httpdomain, sphinx-tabs, sphinx_rtd_theme, sphinx-prompt, sphinx-intl, sphinx-autobuild, mdit-py-plugins, myst_parser Attempting uninstall: Pygments Found existing installation: Pygments 2.17.2 Uninstalling Pygments-2.17.2: Successfully uninstalled Pygments-2.17.2 Attempting uninstall: docutils Found existing installation: docutils 0.20.1 Uninstalling docutils-0.20.1: Successfully uninstalled docutils-0.20.1 Attempting uninstall: Sphinx Found existing installation: Sphinx 7.2.6 Uninstalling Sphinx-7.2.6: Successfully uninstalled Sphinx-7.2.6 Successfully installed Pygments-2.11.2 Sphinx-4.4.0 click-8.1.7 colorama-0.4.6 docutils-0.16 livereload-2.6.3 markdown-it-py-2.2.0 mdit-py-plugins-0.3.5 mdurl-0.1.2 myst_parser-0.16.1 pyyaml-6.0.1 readthedocs-sphinx-search-0.1.1 rstcheck-3.3.1 six-1.16.0 sphinx-autobuild-2021.3.14 sphinx-intl-2.0.1 sphinx-notfound-page-0.8 sphinx-prompt-1.4.0 sphinx-tabs-3.2.0 sphinx_rtd_theme-1.0.0 sphinxcontrib-httpdomain-1.8.0 sphinxemoji-0.2.0 tornado-6.4 [rtd-command-info] start-time: 2024-01-16T20:17:16.163066Z, end-time: 2024-01-16T20:17:16.225415Z, 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("..", ".."))) #sys.path.insert(0, os.path.abspath('..')) #sys.path.append(os.path.dirname(__file__)) #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.duration', 'sphinx.ext.doctest', 'sphinx.ext.autodoc', 'sphinx_tabs.tabs', 'sphinx-prompt', 'sphinx_search.extension', 'sphinx.ext.autosummary', 'sphinx.ext.intersphinx', 'sphinxemoji.sphinxemoji' ] 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'] # 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 = ["build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"] # -- 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' html_static_path = ["_static"] 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_logo = "_static/tigerfish.png" ########################################################################### # 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') # Define this variable in case it's not defined by the user. # It defaults to `alabaster` which is the default from Sphinx. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme html_theme = globals().get('html_theme', 'alabaster') #Add project information to the template context. context = { '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", 'proxied_static_path': "/_/static/", 'versions': [ ("latest", "/en/latest/"), ("stable", "/en/stable/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'beliveau-lab-tigerfish', 'name': u'TigerFISH', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', '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': '8685e8a3', } # 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 '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/1953758/' 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: 2024-01-16T20:17:16.338628Z, end-time: 2024-01-16T20:17:16.880946Z, duration: 0, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v4.4.0 loading translations [en]... done Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages/sphinx/registry.py", line 446, in load_extension metadata = setup(app) ^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages/sphinxcontrib/applehelp/__init__.py", line 230, in setup app.require_sphinx('5.0') File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 400, in require_sphinx raise VersionRequirementError(version) sphinx.errors.VersionRequirementError: 5.0 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/python3.11/site-packages/sphinx/cmd/build.py", line 280, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 226, in __init__ self.setup_extension(extension) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages/sphinx/application.py", line 387, in setup_extension self.registry.load_extension(self, extname) File "/home/docs/checkouts/readthedocs.org/user_builds/beliveau-lab-tigerfish/envs/latest/lib/python3.11/site-packages/sphinx/registry.py", line 449, in load_extension raise VersionRequirementError( sphinx.errors.VersionRequirementError: The sphinxcontrib.applehelp extension used by this project needs at least Sphinx v5.0; it therefore cannot be built with this version. Sphinx version error: The sphinxcontrib.applehelp extension used by this project needs at least Sphinx v5.0; it therefore cannot be built with this version.