Read the Docs build information
Build id: 1340432
Project: icb-anndata
Version: 947
Commit: 6d13c82702e37016c6ed2c09b09916f39b51294f
Date: 2023-03-09T14:22:29.267044Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-03-09T14:22:31.076229Z, end-time: 2023-03-09T14:22:32.172073Z, 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: 2023-03-09T14:22:32.371110Z, end-time: 2023-03-09T14:22:33.185421Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/947/head:external-947
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/947/head -> external-947

[rtd-command-info] start-time: 2023-03-09T14:22:33.394892Z, end-time: 2023-03-09T14:22:33.490134Z, duration: 0, exit-code: 0
git checkout --force 6d13c82702e37016c6ed2c09b09916f39b51294f
Note: switching to '6d13c82702e37016c6ed2c09b09916f39b51294f'.

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 <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 6d13c82 (chore): revert erroneous comment change

[rtd-command-info] start-time: 2023-03-09T14:22:33.740284Z, end-time: 2023-03-09T14:22:33.817263Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-03-09T14:22:34.011053Z, end-time: 2023-03-09T14:22:34.101716Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2023-03-09T14:22:34.317472Z, end-time: 2023-03-09T14:22:34.965589Z, duration: 0, exit-code: 0
git submodule update --init --force --recursive docs/tutorials/notebooks
Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2023-03-09T14:22:41.714144Z, end-time: 2023-03-09T14:22:41.800682Z, duration: 0, exit-code: 0
asdf global python 3.10.8


[rtd-command-info] start-time: 2023-03-09T14:22:42.361673Z, end-time: 2023-03-09T14:22:43.315291Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.10.8.final.0-64 in 641ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947, 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: 2023-03-09T14:22:43.544691Z, end-time: 2023-03-09T14:22:54.695695Z, duration: 11, 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/947/lib/python3.10/site-packages (21.2.3)
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    Uninstalling setuptools-57.4.0:
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    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
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Successfully installed pip-23.0.1 setuptools-58.2.0

[rtd-command-info] start-time: 2023-03-09T14:22:54.874250Z, end-time: 2023-03-09T14:23:05.875627Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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  Preparing metadata (setup.py): started
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Building wheels for collected packages: mock
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Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.2 Pygments-2.14.0 alabaster-0.7.13 babel-2.12.1 certifi-2022.12.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.0 pillow-9.4.0 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.28.2 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 urllib3-1.26.14

[rtd-command-info] start-time: 2023-03-09T14:23:06.139127Z, end-time: 2023-03-09T14:23:59.057682Z, duration: 52, 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/947
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  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5051 sha256=a591a727c59ada853fdbbc11ae0217ee477e61410a9e6998af139a2c6ed85554
  Stored in directory: /tmp/pip-ephem-wheel-cache-1wiz3gi9/wheels/7f/4e/be/1171b40f43b918087657ec57cf3b81fa1a2e027d8755baa184
Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, pickleshare, mistune, fastjsonschema, executing, backcall, asciitree, typing-extensions, traitlets, tornado, tinycss2, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, setuptools, pyzmq, pyyaml, python-dateutil, pyrsistent, pyparsing, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, mdurl, kiwisolver, jupyterlab-pygments, Jinja2, fonttools, fasteners, entrypoints, dunamai, docutils, defusedxml, decorator, cycler, bleach, attrs, asttokens, stack-data, sphinxcontrib-jquery, sphinx, scipy, pandas, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jsonschema, jedi, h5py, get_version, contourpy, beautifulsoup4, awkward-cpp, zarr, sphinx-rtd-theme, sphinx_issues, sphinx-autodoc-typehints, scanpydoc, nbformat, mdit-py-plugins, matplotlib, jupyter-client, IPython, awkward, anndata, sphinxext.opengraph, nbclient, myst_parser, nbconvert, nbsphinx
  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 3.0.3
    Uninstalling Jinja2-3.0.3:
      Successfully uninstalled Jinja2-3.0.3
  Attempting uninstall: docutils
    Found existing installation: docutils 0.17.1
    Uninstalling docutils-0.17.1:
      Successfully uninstalled docutils-0.17.1
  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 IPython-8.11.0 Jinja2-3.1.2 anndata-0.9.0rc2.dev47+g6d13c82 asciitree-0.3.3 asttokens-2.2.1 attrs-22.2.0 awkward-2.1.0 awkward-cpp-12 backcall-0.2.0 beautifulsoup4-4.11.2 bleach-6.0.0 contourpy-1.0.7 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 docutils-0.18.1 dunamai-1.16.0 entrypoints-0.4 executing-1.2.0 fasteners-0.18 fastjsonschema-2.16.3 fonttools-4.39.0 get_version-3.5.4 h5py-3.8.0 jedi-0.18.2 jsonschema-4.17.3 jupyter-client-8.0.3 jupyter-core-5.2.0 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 markdown-it-py-2.2.0 matplotlib-3.7.1 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.5 mdurl-0.1.2 mistune-2.0.5 myst_parser-1.0.0 natsort-8.3.1 nbclient-0.7.2 nbconvert-7.2.9 nbformat-5.7.3 nbsphinx-0.8.12 numcodecs-0.11.0 numpy-1.24.2 pandas-1.5.3 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.1.0 prompt-toolkit-3.0.38 ptyprocess-0.7.0 pure-eval-0.2.2 pyparsing-3.0.9 pyrsistent-0.19.3 python-dateutil-2.8.2 pytz-2022.7.1 pyyaml-6.0 pyzmq-25.0.0 scanpydoc-0.7.7 scipy-1.10.1 setuptools-67.6.0 soupsieve-2.4 sphinx-6.1.3 sphinx-autodoc-typehints-1.22 sphinx-rtd-theme-1.2.0 sphinx_issues-3.0.1 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jquery-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext.opengraph-0.8.1 stack-data-0.6.2 tinycss2-1.2.1 tornado-6.2 traitlets-5.9.0 typing-extensions-4.5.0 wcwidth-0.2.6 webencodings-0.5.1 zarr-2.14.2

[rtd-command-info] start-time: 2023-03-09T14:24:00.662326Z, end-time: 2023-03-09T14:24:00.727402Z, 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", ".md"]
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/notebooks/*.rst",
]
pygments_style = "sphinx"

extensions = [
    "myst_parser",
    "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
    "sphinx_issues",
    "sphinxext.opengraph",
    "scanpydoc",
    "nbsphinx",
    "IPython.sphinxext.ipython_console_highlighting",
]
myst_enable_extensions = [
    "html_image",  # So README.md can be used on github and sphinx docs
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
issues_github_path = "scverse/anndata"
# 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",
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
]


def setup(app: Sphinx):
    # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead.
    app.warningiserror = False


intersphinx_mapping = dict(
    h5py=("https://docs.h5py.org/en/latest/", None),
    hdf5plugin=("https://hdf5plugin.readthedocs.io/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",
    "h5py._hl.dataset.Dataset": "h5py.Dataset",
    "anndata._core.anndata.AnnData": "anndata.AnnData",
}

# -- Social cards ---------------------------------------------------------

ogp_site_url = "https://anndata.readthedocs.io/"
ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg"

# -- 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="main",  # 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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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': "947",
    'version_slug': "947",
    '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': '6d13c82702e37016c6ed2c09b09916f39b51294f',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '6d13c82702e37016c6ed2c09b09916f39b51294f',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '6d13c82702e37016c6ed2c09b09916f39b51294f',
    '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': '6d13c827',
}

# 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/947'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/1340432/'

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: 2023-03-09T14:24:00.916069Z, end-time: 2023-03-09T14:25:12.780041Z, duration: 71, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v6.1.3
Matplotlib is building the font cache; this may take a moment.
making output directory... done
myst v1.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, 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)
loading intersphinx inventory from https://docs.h5py.org/en/latest/objects.inv...
loading intersphinx inventory from https://hdf5plugin.readthedocs.io/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...
intersphinx inventory has moved: https://xarray.pydata.org/en/stable/objects.inv -> https://docs.xarray.dev/en/stable/objects.inv
[autosummary] generating autosummary for: _key_contributors.rst, api.md, benchmark-read-write.ipynb, benchmarks.md, concatenation.rst, contributing.md, fileformat-prose.md, index.md, interoperability.md, news.md, ..., release-notes/index.md, release-notes/release-latest.md, tutorials/index.md, tutorials/notebooks/anncollection-annloader.ipynb, tutorials/notebooks/anncollection.ipynb, tutorials/notebooks/anndata_dask_array.ipynb, tutorials/notebooks/annloader.ipynb, tutorials/notebooks/awkward-arrays.ipynb, tutorials/notebooks/getting-started.ipynb, tutorials/notebooks/{read,write}_dispatched.ipynb
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnLoader.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.IOSpec.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.iterate_axis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.AnnCollection.to_adata.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.IOSpec.encoding_type.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/generated/anndata.experimental.IOSpec.encoding_version.rst
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