Read the Docs build information Build id: 987225 Project: icb-anndata Version: 785 Commit: 26c1bc7b0071a6330ca397034a8c5443cb6464d7 Date: 2022-06-22T12:57:40.514273Z State: finished Success: False [rtd-command-info] start-time: 2022-06-22T12:59:07.432568Z, end-time: 2022-06-22T12:59:08.634033Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/scverse/anndata.git . Cloning into '.'... [rtd-command-info] start-time: 2022-06-22T12:59:08.827118Z, end-time: 2022-06-22T12:59:09.417757Z, duration: 0, exit-code: 0 git fetch origin --force --tags --prune --prune-tags --depth 50 pull/785/head:external-785 From https://github.com/scverse/anndata * [new ref] refs/pull/785/head -> external-785 [rtd-command-info] start-time: 2022-06-22T12:59:09.636246Z, end-time: 2022-06-22T12:59:09.771976Z, duration: 0, exit-code: 0 git checkout --force 26c1bc7b0071a6330ca397034a8c5443cb6464d7 Note: switching to '26c1bc7b0071a6330ca397034a8c5443cb6464d7'. 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 26c1bc7 Update notebook with new benchmark [rtd-command-info] start-time: 2022-06-22T12:59:09.979939Z, end-time: 2022-06-22T12:59:10.076988Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2022-06-22T12:59:16.127896Z, end-time: 2022-06-22T12:59:16.201537Z, duration: 0, exit-code: 0 asdf global python 3.9.13 [rtd-command-info] start-time: 2022-06-22T12:59:16.691785Z, end-time: 2022-06-22T12:59:17.776105Z, duration: 1, exit-code: 0 python -mvirtualenv created virtual environment CPython3.9.13.final.0-64 in 756ms creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785, 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==21.2.3, setuptools==57.4.0, wheel==0.37.0 activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator [rtd-command-info] start-time: 2022-06-22T12:59:17.968772Z, end-time: 2022-06-22T12:59:30.253352Z, duration: 12, 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/icb-anndata/envs/785/lib/python3.9/site-packages (21.2.3) Collecting pip Downloading pip-22.1.2-py3-none-any.whl (2.1 MB) Requirement already satisfied: setuptools<58.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/site-packages (57.4.0) Collecting setuptools<58.3.0 Downloading setuptools-58.2.0-py3-none-any.whl (946 kB) Installing collected packages: setuptools, pip Attempting uninstall: setuptools Found existing installation: setuptools 57.4.0 Uninstalling setuptools-57.4.0: Successfully uninstalled setuptools-57.4.0 Attempting uninstall: pip Found existing installation: pip 21.2.3 Uninstalling pip-21.2.3: Successfully uninstalled pip-21.2.3 Successfully installed pip-22.1.2 setuptools-58.2.0 [rtd-command-info] start-time: 2022-06-22T12:59:30.587122Z, end-time: 2022-06-22T13:00:11.976925Z, duration: 41, 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<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 jinja2<3.1.0 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 861.9/861.9 kB 33.0 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.tar.gz (16.0 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.0/16.0 MB 104.4 MB/s eta 0:00:00 Preparing metadata (setup.py): started Preparing metadata (setup.py): finished with status 'done' 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 112.0 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<2 Downloading Sphinx-1.8.6-py2.py3-none-any.whl (3.1 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 162.1 MB/s eta 0:00:00 Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 6.4/6.4 MB 106.7 MB/s eta 0:00:00 Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.8-py2.py3-none-any.whl (11 kB) Collecting jinja2<3.1.0 Downloading Jinja2-3.0.3-py3-none-any.whl (133 kB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 133.6/133.6 kB 157.5 MB/s eta 0:00:00 Collecting future Downloading future-0.18.2.tar.gz (829 kB) 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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=23772 sha256=53f96531ae5eed530aa07e199f081ae4b2798d52f26b9a915a0e396f8bffd1dc Stored in directory: /tmp/pip-ephem-wheel-cache-w2qfp9zx/wheels/44/dc/c7/e89296d3612588db0aa6545ee3305c23b7a48b3a9922916e1f Building wheel for pillow (setup.py): started Building wheel for pillow (setup.py): finished with status 'done' Created wheel for pillow: filename=Pillow-5.4.1-cp39-cp39-linux_x86_64.whl size=1361235 sha256=431861324cdf9e4cffae29b260a5d1ea1c3209a665eb9efd6cb8744d0e94e8ca Stored in directory: /tmp/pip-ephem-wheel-cache-w2qfp9zx/wheels/d3/de/21/f0ad1b0453288616d3f4d2ce28431aa7a2adde8f27c9b7a0af 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=5daa2261ba7d5d0760334b73ed57d5c8676ec4177c60be8ece70576603ae175d Stored in directory: /tmp/pip-ephem-wheel-cache-w2qfp9zx/wheels/2f/a0/d3/4030d9f80e6b3be787f19fc911b8e7aa462986a40ab1e4bb94 Successfully built mock pillow future Installing collected packages: snowballstemmer, pytz, mock, alabaster, urllib3, sphinxcontrib-serializinghtml, six, pyparsing, Pygments, pillow, MarkupSafe, imagesize, idna, future, docutils, charset-normalizer, certifi, babel, sphinxcontrib-websupport, requests, packaging, jinja2, commonmark, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark Successfully installed MarkupSafe-2.1.1 Pygments-2.12.0 alabaster-0.7.12 babel-2.10.3 certifi-2022.6.15 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2022.1 readthedocs-sphinx-ext-2.1.8 recommonmark-0.5.0 requests-2.28.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.9 [rtd-command-info] start-time: 2022-06-22T13:00:12.265325Z, end-time: 2022-06-22T13:00:53.982034Z, duration: 41, exit-code: 0 python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc] Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785 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' Installing backend dependencies: started Installing backend dependencies: finished with status 'done' Preparing metadata (pyproject.toml): started Preparing metadata (pyproject.toml): finished with status 'done' Collecting pandas>=1.1.1 Downloading pandas-1.4.2-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.7 MB) ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 11.7/11.7 MB 190.5 MB/s eta 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Stored in directory: /tmp/pip-ephem-wheel-cache-gdvi5gjf/wheels/89/3c/b7/088212803ae1e1ebe11f896a5cb446842f826223b4a1513722 Building wheel for asciitree (setup.py): started Building wheel for asciitree (setup.py): finished with status 'done' Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5051 sha256=013760fd96e8bcb06205910c7779ebcaa37e0396bcd1e393567c8910a5ef1def Stored in directory: /tmp/pip-ephem-wheel-cache-gdvi5gjf/wheels/07/00/bc/937e878be0d781a569792a1e0e5acf149e463d4536453ec978 Successfully built anndata asciitree Installing collected packages: webencodings, mistune, fastjsonschema, asciitree, zipp, traitlets, tornado, tinycss2, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, pyzmq, python-dateutil, pyrsistent, pandocfilters, numpy, nest-asyncio, natsort, jupyterlab-pygments, Jinja2, fasteners, entrypoints, defusedxml, bleach, attrs, scipy, pandas, numcodecs, jupyter-core, jsonschema, importlib-metadata, h5py, dunamai, beautifulsoup4, zarr, sphinx, nbformat, jupyter-client, get_version, anndata, sphinx-rtd-theme, sphinx_issues, sphinx-autodoc-typehints, scanpydoc, nbclient, nbconvert, nbsphinx Attempting uninstall: Jinja2 Found existing installation: Jinja2 3.0.3 Uninstalling Jinja2-3.0.3: Successfully uninstalled Jinja2-3.0.3 Attempting uninstall: sphinx Found existing installation: Sphinx 1.8.6 Uninstalling Sphinx-1.8.6: Successfully uninstalled Sphinx-1.8.6 Attempting uninstall: sphinx-rtd-theme Found existing installation: sphinx-rtd-theme 0.4.3 Uninstalling sphinx-rtd-theme-0.4.3: Successfully uninstalled sphinx-rtd-theme-0.4.3 Successfully installed Jinja2-3.1.2 anndata-0.9.0.dev9+g26c1bc7 asciitree-0.3.3 attrs-21.4.0 beautifulsoup4-4.11.1 bleach-5.0.0 defusedxml-0.7.1 dunamai-1.12.0 entrypoints-0.4 fasteners-0.17.3 fastjsonschema-2.15.3 get_version-3.5.4 h5py-3.7.0 importlib-metadata-4.11.4 jsonschema-4.6.0 jupyter-client-7.3.4 jupyter-core-4.10.0 jupyterlab-pygments-0.2.2 mistune-0.8.4 natsort-8.1.0 nbclient-0.6.4 nbconvert-6.5.0 nbformat-5.4.0 nbsphinx-0.8.9 nest-asyncio-1.5.5 numcodecs-0.9.1 numpy-1.22.4 pandas-1.4.2 pandocfilters-1.5.0 pyrsistent-0.18.1 python-dateutil-2.8.2 pyzmq-23.2.0 scanpydoc-0.7.7 scipy-1.8.1 soupsieve-2.3.2.post1 sphinx-5.0.2 sphinx-autodoc-typehints-1.18.3 sphinx-rtd-theme-1.0.0 sphinx_issues-3.0.1 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 tinycss2-1.1.1 tornado-6.1 traitlets-5.3.0 webencodings-0.5.1 zarr-2.11.3 zipp-3.8.0 [rtd-command-info] start-time: 2022-06-22T13:00:55.715904Z, end-time: 2022-06-22T13:00:55.783901Z, duration: 0, exit-code: 0 cat docs/conf.py import sys import logging from pathlib import Path from datetime import datetime from sphinx.application import Sphinx HERE = Path(__file__).parent sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")] import anndata # noqa logger = logging.getLogger(__name__) for generated in HERE.glob("anndata.*.rst"): generated.unlink() # -- General configuration ------------------------------------------------ needs_sphinx = "1.7" # autosummary bugfix # General information project = "anndata" author = f"{project} developers" copyright = f"{datetime.now():%Y}, {author}" version = anndata.__version__.replace(".dirty", "") release = version # default settings templates_path = ["_templates"] html_static_path = ["_static"] source_suffix = ".rst" master_doc = "index" default_role = "literal" exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] pygments_style = "sphinx" extensions = [ "sphinx.ext.autodoc", "sphinx.ext.intersphinx", "sphinx.ext.doctest", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.napoleon", "sphinx.ext.autosummary", "sphinx_autodoc_typehints", # needs to be after napoleon "scanpydoc", "nbsphinx", *[p.stem for p in (HERE / "extensions").glob("*.py")], ] # Generate the API documentation when building autosummary_generate = True autodoc_member_order = "bysource" # autodoc_default_flags = ['members'] napoleon_google_docstring = False napoleon_numpy_docstring = True napoleon_include_init_with_doc = False napoleon_use_rtype = True # having a separate entry generally helps readability napoleon_use_param = True napoleon_custom_sections = [("Params", "Parameters")] typehints_defaults = "braces" todo_include_todos = False nitpicky = True # Report broken links nitpick_ignore = [ ("py:class", "scipy.sparse.base.spmatrix"), ("py:meth", "pandas.DataFrame.iloc"), ("py:meth", "pandas.DataFrame.loc"), ("py:class", "anndata._core.views.ArrayView"), ("py:class", "anndata._core.raw.Raw"), *[ ("py:class", f"anndata._core.aligned_mapping.{cls}{kind}") for cls in "Layers AxisArrays PairwiseArrays".split() for kind in ["", "View"] ], ] suppress_warnings = ["ref.citation"] def setup(app: Sphinx): # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead. app.warningiserror = True intersphinx_mapping = dict( h5py=("https://docs.h5py.org/en/latest/", None), loompy=("https://linnarssonlab.org/loompy/", None), numpy=("https://numpy.org/doc/stable/", None), pandas=("https://pandas.pydata.org/pandas-docs/stable/", None), python=("https://docs.python.org/3", None), scipy=("https://docs.scipy.org/doc/scipy/", None), sklearn=("https://scikit-learn.org/stable/", None), zarr=("https://zarr.readthedocs.io/en/stable/", None), xarray=("https://xarray.pydata.org/en/stable/", None), ) qualname_overrides = { "h5py._hl.group.Group": "h5py.Group", "h5py._hl.files.File": "h5py.File", "anndata._core.anndata.AnnData": "anndata.AnnData", } # -- Options for HTML output ---------------------------------------------- html_theme = "scanpydoc" html_theme_options = dict(navigation_depth=4) html_context = dict( display_github=True, # Integrate GitHub github_user="scverse", # Username github_repo="anndata", # Repo name github_version="master", # Version conf_py_path="/docs/", # Path in the checkout to the docs root ) issues_github_path = "{github_user}/{github_repo}".format_map(html_context) html_show_sphinx = False # -- Options for other output formats ------------------------------------------ htmlhelp_basename = f"{project}doc" doc_title = f"{project} Documentation" latex_documents = [(master_doc, f"{project}.tex", doc_title, author, "manual")] man_pages = [(master_doc, project, doc_title, [author], 1)] texinfo_documents = [ ( master_doc, project, doc_title, author, project, "One line description of project.", "Miscellaneous", ) ] ########################################################################### # 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': "785", 'version_slug': "785", '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/"), ("0.7.8", "/en/0.7.8/"), ("0.4.1", "/en/0.4.1/"), ("0.3", "/en/0.3/"), ], 'downloads': [ ], 'subprojects': [ ], 'slug': 'icb-anndata', 'name': u'anndata', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://anndata.readthedocs.io/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/docs/', 'api_host': 'https://readthedocs.com', 'github_user': 'scverse', 'proxied_api_host': '/_', 'github_repo': 'anndata', 'github_version': '26c1bc7b0071a6330ca397034a8c5443cb6464d7', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': '26c1bc7b0071a6330ca397034a8c5443cb6464d7', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': '26c1bc7b0071a6330ca397034a8c5443cb6464d7', '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': '26c1bc7b', } # 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 'external' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'https://github.com/scverse/anndata/pull/785' readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/987225/' 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: 2022-06-22T13:00:55.995618Z, end-time: 2022-06-22T13:01:07.466497Z, duration: 11, exit-code: 2 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v5.0.2 making output directory... done loading intersphinx inventory from https://docs.h5py.org/en/latest/objects.inv... loading intersphinx inventory from https://linnarssonlab.org/loompy/objects.inv... loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv... loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv... loading intersphinx inventory from https://docs.python.org/3/objects.inv... loading intersphinx inventory from https://docs.scipy.org/doc/scipy/objects.inv... loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv... loading intersphinx inventory from https://zarr.readthedocs.io/en/stable/objects.inv... loading intersphinx inventory from https://xarray.pydata.org/en/stable/objects.inv... [autosummary] generating autosummary for: _key_contributors.rst, api.rst, benchmark-comparitive.ipynb, benchmark-read-write.ipynb, benchmarks.rst, concatenation.rst, contributing.rst, fileformat-prose.rst, index.rst, news.rst, ..., release-notes/0.7.5.rst, release-notes/0.7.6.rst, release-notes/0.7.7.rst, release-notes/0.7.8.rst, release-notes/0.8.0.rst, release-notes/0.8.1.rst, release-notes/0.9.0.rst, release-notes/index.rst, release-notes/release-latest.rst, tutorials.rst /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/anndata/experimental/pytorch/_annloader.py:18: UserWarning: Сould not load pytorch. warnings.warn("Сould not load pytorch.") [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnLoader.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.read_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.read_zarr.rst [autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.convert.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.has_backed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.iterate_axis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/generated/anndata.experimental.AnnCollection.to_adata.rst building [mo]: targets for 0 po files that are out of date building [html]: targets for 28 source files that are out of date updating environment: [new config] 97 added, 0 changed, 0 removed reading sources... [ 1%] _key_contributors reading sources... [ 2%] api reading sources... [ 3%] benchmark-comparitive reading sources... [ 4%] benchmark-read-write reading sources... [ 5%] benchmarks reading sources... [ 6%] concatenation reading sources... [ 7%] contributing reading sources... [ 8%] fileformat-prose reading sources... [ 9%] generated/anndata.AnnData reading sources... [ 10%] generated/anndata.AnnData.T reading sources... [ 11%] generated/anndata.AnnData.X reading sources... [ 12%] generated/anndata.AnnData.chunk_X reading sources... [ 13%] generated/anndata.AnnData.chunked_X reading sources... [ 14%] generated/anndata.AnnData.concatenate reading sources... [ 15%] generated/anndata.AnnData.copy reading sources... [ 16%] generated/anndata.AnnData.filename reading sources... [ 17%] generated/anndata.AnnData.is_view reading sources... [ 18%] generated/anndata.AnnData.isbacked reading sources... [ 19%] generated/anndata.AnnData.layers reading sources... [ 20%] generated/anndata.AnnData.n_obs reading sources... [ 21%] generated/anndata.AnnData.n_vars reading sources... [ 22%] generated/anndata.AnnData.obs reading sources... [ 23%] generated/anndata.AnnData.obs_keys reading sources... [ 24%] generated/anndata.AnnData.obs_names reading sources... [ 25%] generated/anndata.AnnData.obs_names_make_unique reading sources... [ 26%] generated/anndata.AnnData.obs_vector reading sources... [ 27%] generated/anndata.AnnData.obsm reading sources... [ 28%] generated/anndata.AnnData.obsm_keys reading sources... [ 29%] generated/anndata.AnnData.obsp reading sources... [ 30%] generated/anndata.AnnData.raw reading sources... [ 31%] generated/anndata.AnnData.rename_categories reading sources... [ 32%] generated/anndata.AnnData.shape reading sources... [ 34%] generated/anndata.AnnData.strings_to_categoricals reading sources... [ 35%] generated/anndata.AnnData.to_df reading sources... [ 36%] generated/anndata.AnnData.to_memory reading sources... [ 37%] generated/anndata.AnnData.transpose reading sources... [ 38%] generated/anndata.AnnData.uns reading sources... [ 39%] generated/anndata.AnnData.uns_keys reading sources... [ 40%] generated/anndata.AnnData.var reading sources... [ 41%] generated/anndata.AnnData.var_keys reading sources... [ 42%] generated/anndata.AnnData.var_names reading sources... [ 43%] generated/anndata.AnnData.var_names_make_unique reading sources... [ 44%] generated/anndata.AnnData.var_vector reading sources... [ 45%] generated/anndata.AnnData.varm reading sources... [ 46%] generated/anndata.AnnData.varm_keys reading sources... [ 47%] generated/anndata.AnnData.varp reading sources... [ 48%] generated/anndata.AnnData.write reading sources... [ 49%] generated/anndata.AnnData.write_csvs reading sources... [ 50%] generated/anndata.AnnData.write_h5ad reading sources... [ 51%] generated/anndata.AnnData.write_loom reading sources... [ 52%] generated/anndata.AnnData.write_zarr reading sources... [ 53%] generated/anndata.ImplicitModificationWarning reading sources... [ 54%] generated/anndata.concat reading sources... [ 55%] generated/anndata.experimental.AnnCollection reading sources... [ 56%] generated/anndata.experimental.AnnCollection.attrs_keys reading sources... [ 57%] generated/anndata.experimental.AnnCollection.convert reading sources... [ 58%] generated/anndata.experimental.AnnCollection.has_backed reading sources... [ 59%] generated/anndata.experimental.AnnCollection.iterate_axis reading sources... [ 60%] generated/anndata.experimental.AnnCollection.lazy_attr reading sources... [ 61%] generated/anndata.experimental.AnnCollection.n_obs reading sources... [ 62%] generated/anndata.experimental.AnnCollection.n_vars reading sources... [ 63%] generated/anndata.experimental.AnnCollection.obs reading sources... [ 64%] generated/anndata.experimental.AnnCollection.obsm reading sources... [ 65%] generated/anndata.experimental.AnnCollection.shape reading sources... [ 67%] generated/anndata.experimental.AnnCollection.to_adata reading sources... [ 68%] generated/anndata.experimental.AnnLoader reading sources... [ 69%] generated/anndata.experimental.read_elem reading sources... [ 70%] generated/anndata.experimental.write_elem reading sources... [ 71%] generated/anndata.read_csv reading sources... [ 72%] generated/anndata.read_excel reading sources... [ 73%] generated/anndata.read_h5ad reading sources... [ 74%] generated/anndata.read_hdf reading sources... [ 75%] generated/anndata.read_loom reading sources... [ 76%] generated/anndata.read_mtx reading sources... [ 77%] generated/anndata.read_text reading sources... [ 78%] generated/anndata.read_umi_tools reading sources... [ 79%] generated/anndata.read_zarr reading sources... [ 80%] index reading sources... [ 81%] news reading sources... [ 82%] references reading sources... [ 83%] release-notes/0.4.0 reading sources... [ 84%] release-notes/0.5.0 reading sources... [ 85%] release-notes/0.6.0 reading sources... [ 86%] release-notes/0.7.0 reading sources... [ 87%] release-notes/0.7.2 reading sources... [ 88%] release-notes/0.7.3 reading sources... [ 89%] release-notes/0.7.4 reading sources... [ 90%] release-notes/0.7.5 reading sources... [ 91%] release-notes/0.7.6 reading sources... [ 92%] release-notes/0.7.7 reading sources... [ 93%] release-notes/0.7.8 reading sources... [ 94%] release-notes/0.8.0 reading sources... [ 95%] release-notes/0.8.1 reading sources... [ 96%] release-notes/0.9.0 reading sources... [ 97%] release-notes/index reading sources... [ 98%] release-notes/release-latest reading sources... [100%] tutorials looking for now-outdated files... none found pickling environment... done checking consistency... failed Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/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/icb-anndata/envs/785/lib/python3.9/site-packages/sphinx/application.py", line 329, in build self.builder.build_update() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 288, in build_update self.build(to_build, File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/site-packages/sphinx/builders/__init__.py", line 324, in build self.env.check_consistency() File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/site-packages/sphinx/environment/__init__.py", line 630, in check_consistency logger.warning(__('document isn\'t included in any toctree'), File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 1812, in warning self.log(WARNING, msg, *args, **kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/site-packages/sphinx/util/logging.py", line 122, in log super().log(level, msg, *args, **kwargs) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 1844, in log self.logger.log(level, msg, *args, **kwargs) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 1512, in log self._log(level, msg, args, **kwargs) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 1589, in _log self.handle(record) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 1599, in handle self.callHandlers(record) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 1661, in callHandlers hdlr.handle(record) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 948, in handle rv = self.filter(record) File "/home/docs/.asdf/installs/python/3.9.13/lib/python3.9/logging/__init__.py", line 806, in filter result = f.filter(record) File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/785/lib/python3.9/site-packages/sphinx/util/logging.py", line 425, in filter raise exc sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/benchmark-comparitive.ipynb:document isn't included in any toctree Warning, treated as error: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/785/docs/benchmark-comparitive.ipynb:document isn't included in any toctree