Read the Docs build information Build id: 2185757 Project: icb-scanpy-tutorials Version: latest Commit: 5055846a1bb56bc10699751f951963df4f6d7134 Date: 2024-04-30T07:47:18.516476Z State: finished Success: True [rtd-command-info] start-time: 2024-04-30T07:47:19.731401Z, end-time: 2024-04-30T07:47:25.939227Z, duration: 6, exit-code: 0 git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git . Cloning into '.'... [rtd-command-info] start-time: 2024-04-30T07:47:26.003681Z, end-time: 2024-04-30T07:47:42.364667Z, duration: 16, exit-code: 0 git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main [rtd-command-info] start-time: 2024-04-30T07:47:42.492425Z, end-time: 2024-04-30T07:47:43.052827Z, duration: 0, exit-code: 0 git checkout --force origin/main Note: switching to 'origin/main'. 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 5055846 [pre-commit.ci] pre-commit autoupdate (#107) [rtd-command-info] start-time: 2024-04-30T07:47:43.121192Z, end-time: 2024-04-30T07:47:43.187207Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2024-04-30T07:47:43.252673Z, end-time: 2024-04-30T07:47:43.306340Z, duration: 0, exit-code: 0 cat .readthedocs.yml version: 2 build: os: ubuntu-22.04 tools: python: "3.12" sphinx: configuration: conf.py python: install: - method: pip path: . [rtd-command-info] start-time: 2024-04-30T07:47:49.444634Z, end-time: 2024-04-30T07:47:49.536882Z, duration: 0, exit-code: 0 asdf global python 3.12.0 [rtd-command-info] start-time: 2024-04-30T07:47:49.940940Z, end-time: 2024-04-30T07:47:51.108957Z, duration: 1, exit-code: 0 python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH created virtual environment CPython3.12.0.final.0-64 in 858ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/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: 2024-04-30T07:47:51.182123Z, end-time: 2024-04-30T07:48:03.548974Z, duration: 12, exit-code: 0 python -m pip 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Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest 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==0.1.dev50+g5055846) Downloading myst_nb-1.1.0-py3-none-any.whl.metadata (4.7 kB) Collecting scanpydoc>=0.13.4 (from scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+g5055846) 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/latest/lib/python3.12/site-packages (from scanpy-tutorials==0.1.dev50+g5055846) (7.3.7) Collecting sphinx-book-theme>=1.1.0 (from 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/tmp/pip-ephem-wheel-cache-942qctdq/wheels/51/e4/74/d5b179a00fb7ad0cbe07174ffc636dbd50a844179d11a6534c Successfully built scanpy-tutorials Installing collected packages: wcwidth, pure-eval, ptyprocess, fastjsonschema, zipp, typing-extensions, traitlets, tornado, tabulate, soupsieve, six, rpds-py, pyzmq, pyyaml, psutil, prompt-toolkit, platformdirs, pexpect, parso, nest-asyncio, mdurl, greenlet, executing, decorator, debugpy, click, attrs, accessible-pygments, sqlalchemy, referencing, python-dateutil, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, comm, beautifulsoup4, asttokens, stack-data, scanpydoc, pydata-sphinx-theme, mdit-py-plugins, jupyter-client, jsonschema-specifications, sphinx-book-theme, myst-parser, jsonschema, ipython, nbformat, ipykernel, nbclient, jupyter-cache, myst-nb, scanpy-tutorials Successfully installed accessible-pygments-0.0.4 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.3 click-8.1.7 comm-0.2.2 debugpy-1.8.1 decorator-5.1.1 executing-2.0.1 fastjsonschema-2.19.1 greenlet-3.0.3 importlib_metadata-7.1.0 ipykernel-6.29.4 ipython-8.24.0 jedi-0.19.1 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.1 jupyter-core-5.7.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.0 mdurl-0.1.2 myst-nb-1.1.0 myst-parser-3.0.1 nbclient-0.10.0 nbformat-5.10.4 nest-asyncio-1.6.0 parso-0.8.4 pexpect-4.9.0 platformdirs-4.2.1 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 python-dateutil-2.9.0.post0 pyyaml-6.0.1 pyzmq-26.0.2 referencing-0.35.0 rpds-py-0.18.0 scanpy-tutorials-0.1.dev50+g5055846 scanpydoc-0.13.4 six-1.16.0 soupsieve-2.5 sphinx-book-theme-1.1.2 sqlalchemy-2.0.29 stack-data-0.6.3 tabulate-0.9.0 tornado-6.4 traitlets-5.14.3 typing-extensions-4.11.0 wcwidth-0.2.13 zipp-3.18.1 [rtd-command-info] start-time: 2024-04-30T07:48:38.212977Z, end-time: 2024-04-30T07:48:38.273731Z, duration: 0, exit-code: 0 cat conf.py from datetime import datetime from importlib.metadata import metadata from sphinx.application import Sphinx from myst_nb.core.render import NbElementRenderer, MimeData from docutils import nodes 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_execution_mode = "off" nb_output_stderr = "remove" myst_heading_anchors = 3 render_image_orig = NbElementRenderer.render_image def render_image(self: NbElementRenderer, data: MimeData) -> list[nodes.Element]: """Makes images display size default to their jupyter setting. Workaround for: https://github.com/executablebooks/MyST-NB/issues/522 """ node_list = render_image_orig(self, data) try: [image] = node_list if not isinstance(image, nodes.image): raise ValueError(f"Expected nodes.image, got {type(image)}") for key in ("width", "height"): if key in image: continue if (v := data.output_metadata.get(data.mime_type, {}).get(key)) is None: continue image[key] = str(v) except Exception: return node_list return [image] def setup(app: Sphinx) -> None: if NbElementRenderer.render_image is render_image_orig: NbElementRenderer.render_image = render_image ########################################################################### # 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/"), ("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': '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': '5055846a', } # 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/icb-scanpy-tutorials/builds/2185757/' 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: 2024-04-30T07:48:38.357486Z, end-time: 2024-04-30T07:48:49.292944Z, duration: 10, exit-code: 0 python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html Running Sphinx v7.3.7 making output directory... done myst v3.0.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True) myst-nb v1.1.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False) Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/_readthedocs/.jupyter_cache The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492 building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 15 source files that are out of date updating environment: [new config] 15 added, 0 changed, 0 removed reading sources... [ 7%] README reading sources... [ 13%] basic-scrna-tutorial reading sources... [ 20%] dask reading sources... [ 27%] index reading sources... [ 33%] integrating-data-using-ingest reading sources... [ 40%] knn-transformers reading sources... [ 47%] paga-paul15 reading sources... [ 53%] pbmc3k reading sources... [ 60%] plotting-with-marsilea reading sources... [ 67%] plotting/advanced reading sources... [ 73%] plotting/core reading sources... 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