Read the Docs build information Build id: 2074889 Project: icb-scanpy-tutorials Version: 86 Commit: 04b9875c635a2c6102929042676506f96e98c028 Date: 2024-03-11T12:50:40.126494Z State: finished Success: False [rtd-command-info] start-time: 2024-03-11T12:50:41.177241Z, end-time: 2024-03-11T12:50:47.136488Z, duration: 5, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2024-03-11T12:50:47.205065Z, end-time: 2024-03-11T12:51:11.715003Z, duration: 24, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 pull/86/head:external-86 From https://github.com/scverse/scanpy-tutorials * [new ref] refs/pull/86/head -> external-86 * [new tag] 1.4.6 -> 1.4.6 [rtd-command-info] start-time: 2024-03-11T12:51:11.858547Z, end-time: 2024-03-11T12:51:12.134545Z, duration: 0, exit-code: 0 git checkout --force 04b9875c635a2c6102929042676506f96e98c028 Note: switching to '04b9875c635a2c6102929042676506f96e98c028'. 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 04b9875 missed one [rtd-command-info] start-time: 2024-03-11T12:51:12.196807Z, end-time: 2024-03-11T12:51:12.261287Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-03-11T12:51:12.334471Z, end-time: 2024-03-11T12:51:12.397770Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-22.04 tools: python: "3.11" sphinx: configuration: conf.py python: install: - method: pip path: . [rtd-command-info] start-time: 2024-03-11T12:51:18.564640Z, end-time: 2024-03-11T12:51:18.646642Z, duration: 0, exit-code: 0 asdf global python 3.11.6 [rtd-command-info] start-time: 2024-03-11T12:51:19.045525Z, end-time: 2024-03-11T12:51:20.125371Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.11.6.final.0-64 in 772ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86, 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: 2024-03-11T12:51:20.194670Z, end-time: 2024-03-11T12:51:31.083667Z, duration: 10, exit-code: 0 python -m pip 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Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/86 Installing build dependencies: started Installing build dependencies: finished with status 'done' Getting requirements to build wheel: started Getting requirements to build wheel: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting myst-nb (from scanpy-tutorials==1.4.7.dev46+g04b9875) Downloading myst_nb-1.0.0-py3-none-any.whl.metadata (4.7 kB) Collecting scanpydoc>=0.13.4 (from scanpy-tutorials==1.4.7.dev46+g04b9875) Downloading scanpydoc-0.13.4-py3-none-any.whl.metadata (2.6 kB) Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages (from scanpy-tutorials==1.4.7.dev46+g04b9875) (7.2.6) Requirement already satisfied: sphinxcontrib-applehelp in 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Building wheel for scanpy-tutorials (pyproject.toml): started Building wheel for scanpy-tutorials (pyproject.toml): finished with status 'done' Created wheel for scanpy-tutorials: filename=scanpy_tutorials-1.4.7.dev46+g04b9875-py3-none-any.whl size=1001 sha256=ff4c243ff72f0c01dc49c273f71f628317e6629b97a5c6e66b06a0fea554470c Stored in directory: /tmp/pip-ephem-wheel-cache-yply2omt/wheels/08/19/a7/0cdeb036b6bcc7838601cbecf93901368fcca07df9217526f0 Successfully built scanpy-tutorials Installing collected packages: wcwidth, pure-eval, ptyprocess, fastjsonschema, zipp, typing-extensions, traitlets, tornado, tabulate, six, rpds-py, pyzmq, pyyaml, psutil, prompt-toolkit, platformdirs, pexpect, parso, nest-asyncio, mdurl, greenlet, executing, decorator, debugpy, click, attrs, sqlalchemy, referencing, python-dateutil, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, comm, asttokens, stack-data, scanpydoc, mdit-py-plugins, jupyter-client, jsonschema-specifications, myst-parser, jsonschema, ipython, nbformat, ipykernel, nbclient, jupyter-cache, myst-nb, scanpy-tutorials Successfully installed asttokens-2.4.1 attrs-23.2.0 click-8.1.7 comm-0.2.1 debugpy-1.8.1 decorator-5.1.1 executing-2.0.1 fastjsonschema-2.19.1 greenlet-3.0.3 importlib_metadata-7.0.2 ipykernel-6.29.3 ipython-8.22.2 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.0 jupyter-core-5.7.1 markdown-it-py-3.0.0 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 myst-nb-1.0.0 myst-parser-2.0.0 nbclient-0.9.0 nbformat-5.9.2 nest-asyncio-1.6.0 parso-0.8.3 pexpect-4.9.0 platformdirs-4.2.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 python-dateutil-2.9.0.post0 pyyaml-6.0.1 pyzmq-25.1.2 referencing-0.33.0 rpds-py-0.18.0 scanpy-tutorials-1.4.7.dev46+g04b9875 scanpydoc-0.13.4 six-1.16.0 sqlalchemy-2.0.28 stack-data-0.6.3 tabulate-0.9.0 tornado-6.4 traitlets-5.14.1 typing-extensions-4.10.0 wcwidth-0.2.13 zipp-3.17.0 [rtd-command-info] start-time: 2024-03-11T12:51:54.646495Z, end-time: 2024-03-11T12:51:54.709497Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime from importlib.metadata import metadata meta = metadata("scanpy-tutorials") project = meta["Name"] author = meta["Author"] copyright = f"{datetime.now():%Y}, {author}" release = version = meta["Version"] extensions = [ "myst_nb", ] myst_enable_extensions = [ "colon_fence", ] templates_path = ["_templates"] source_suffix = ".rst" master_doc = "index" language = "en" exclude_patterns = [ "_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "scanpy_workshop/*", ] pygments_style = "sphinx" # -- Options for HTML output ---------------------------------------------- html_theme = "scanpydoc" html_theme_options = dict( repository_url="https://github.com/theislab/scanpy-tutorials", repository_branch="master", use_repository_button=True, ) html_static_path = ["_static"] html_logo = "_static/img/Scanpy_Logo_BrightFG.svg" # -- Notebook settings ---------------------------------------------------- nb_output_stderr = "remove" myst_heading_anchors = 3 ########################################################################### # 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': "86", 'version_slug': "86", '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/"), ("multiomics", "/en/multiomics/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-scanpy-tutorials', 'name': u'scanpy-tutorials', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': '', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'scanpy-tutorials', 'github_version': '04b9875c635a2c6102929042676506f96e98c028', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '04b9875c635a2c6102929042676506f96e98c028', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '04b9875c635a2c6102929042676506f96e98c028', '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': '04b9875c', } # 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/scverse/scanpy-tutorials/pull/86' readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy-tutorials/builds/2074889/' 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: 2024-03-11T12:51:54.791448Z, end-time: 2024-03-11T12:51:56.118518Z, duration: 1, exit-code: 2 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.2.6 making output directory... done Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/theming.py", line 83, in __init__ self.base = factory.create(inherit) ^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/theming.py", line 230, in create raise ThemeError(__('no theme named %r found (missing theme.conf?)') % name) sphinx.errors.ThemeError: no theme named 'sphinx_book_theme' found (missing theme.conf?) The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/cmd/build.py", line 293, in build_main app = Sphinx(args.sourcedir, args.confdir, args.outputdir, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/application.py", line 272, in __init__ self._init_builder() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/application.py", line 342, in _init_builder self.builder.init() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/builders/html/__init__.py", line 219, in init self.init_templates() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/builders/html/__init__.py", line 270, in init_templates self.theme = theme_factory.create(themename) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/theming.py", line 232, in create return Theme(name, self.themes[name], factory=self) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/86/lib/python3.11/site-packages/sphinx/theming.py", line 85, in __init__ raise ThemeError(__('no theme named %r found, inherited by %r') % sphinx.errors.ThemeError: no theme named 'sphinx_book_theme' found, inherited by 'scanpydoc' Theme error: no theme named 'sphinx_book_theme' found, inherited by 'scanpydoc'