Read the Docs build information
Build id: 1690389
Project: icb-anndata
Version: latest
Commit: 22f33bb27cd54db5654560116cd4dcff4ebf2bc8
Date: 2023-08-29T18:52:33.781076Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-08-29T18:54:03.498284Z, end-time: 2023-08-29T18:54:04.075239Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-08-29T18:54:04.509213Z, end-time: 2023-08-29T18:54:05.144065Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/main:refs/remotes/origin/main


[rtd-command-info] start-time: 2023-08-29T18:54:05.942542Z, end-time: 2023-08-29T18:54:06.012580Z, 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 <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 22f33bb Add new DON'T MERGE check (#1046)

[rtd-command-info] start-time: 2023-08-29T18:54:06.540580Z, end-time: 2023-08-29T18:54:06.597637Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-08-29T18:54:07.161568Z, end-time: 2023-08-29T18:54:07.461795Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2023-08-29T18:54:07.948695Z, end-time: 2023-08-29T18:54:08.669425Z, 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/latest/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2023-08-29T18:54:09.168548Z, end-time: 2023-08-29T18:54:09.231804Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: "3.11"
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true # do not change or you will be fired
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc
submodules:
  include:
    - "docs/tutorials/notebooks"
  recursive: true

[rtd-command-info] start-time: 2023-08-29T18:54:17.333070Z, end-time: 2023-08-29T18:54:17.408511Z, duration: 0, exit-code: 0
asdf global python 3.11.4


[rtd-command-info] start-time: 2023-08-29T18:54:18.299413Z, end-time: 2023-08-29T18:54:19.209389Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.4.final.0-64 in 596ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/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==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-08-29T18:54:19.857538Z, end-time: 2023-08-29T18:54:32.442064Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-68.1.2-py3-none-any.whl (805 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-23.2.1 setuptools-68.1.2

[rtd-command-info] start-time: 2023-08-29T18:54:32.950939Z, end-time: 2023-08-29T18:54:40.860031Z, duration: 7, 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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  Obtaining dependency information for Pygments>=2.0 from https://files.pythonhosted.org/packages/43/88/29adf0b44ba6ac85045e63734ae0997d3c58d8b1a91c914d240828d0d73d/Pygments-2.16.1-py3-none-any.whl.metadata
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages (from sphinx<2) (68.1.2)
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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=0089c84fe7207002a64c87c84c30d7cbaecc41860053867e8ee0641bfeaa5136
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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-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 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 urllib3-2.0.4

[rtd-command-info] start-time: 2023-08-29T18:54:41.731807Z, end-time: 2023-08-29T18:55:20.269092Z, duration: 38, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest
  Installing build dependencies: started
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Building wheels for collected packages: anndata, asciitree
  Building wheel for anndata (pyproject.toml): started
  Building wheel for anndata (pyproject.toml): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.1.dev50+g22f33bb-py3-none-any.whl size=114163 sha256=9f9c5e7cbb7aa44baeec550b023462085fac0af16b7627c9f71934e78a13af16
  Stored in directory: /tmp/pip-ephem-wheel-cache-297vgomx/wheels/ac/78/17/d6beb4bb5885bedd4df2dd7b9cf80e3cd148368110ea659730
  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=5033 sha256=7e675405d3cb247f803542cf1f50386f565384a7b935c5dfd2462b9fa8b08a8e
  Stored in directory: /tmp/pip-ephem-wheel-cache-297vgomx/wheels/71/c1/da/23077eb3b87d24d6f3852ed1ed1a1ac2d3c885ad6ebd2b4a07
Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, pickleshare, fastjsonschema, executing, backcall, asciitree, array-api-compat, tzdata, typing-extensions, traitlets, tornado, tinycss2, sphinxcontrib-jsmath, soupsieve, rpds-py, pyzmq, pyyaml, python-dateutil, pyparsing, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, mistune, mdurl, kiwisolver, jupyterlab-pygments, fonttools, fasteners, entrypoints, docutils, defusedxml, decorator, cycler, bleach, attrs, asttokens, accessible-pygments, stack-data, scipy, referencing, pandas, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, h5py, contourpy, beautifulsoup4, awkward-cpp, zarr, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, awkward, anndata, jsonschema, nbformat, nbclient, nbconvert, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx, pydata-sphinx-theme, sphinxext-opengraph, sphinx-issues, sphinx-copybutton, sphinx-book-theme, sphinx-autodoc-typehints, scanpydoc, nbsphinx, myst-parser
  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
Successfully installed accessible-pygments-0.0.4 anndata-0.1.dev50+g22f33bb array-api-compat-1.3 asciitree-0.3.3 asttokens-2.2.1 attrs-23.1.0 awkward-2.3.3 awkward-cpp-22 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 contourpy-1.1.0 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 docutils-0.19 entrypoints-0.4 executing-1.2.0 fasteners-0.18 fastjsonschema-2.18.0 fonttools-4.42.1 h5py-3.9.0 ipython-8.14.0 jedi-0.19.0 jsonschema-4.19.0 jsonschema-specifications-2023.7.1 jupyter-client-8.3.1 jupyter-core-5.3.1 jupyterlab-pygments-0.2.2 kiwisolver-1.4.5 markdown-it-py-3.0.0 matplotlib-3.7.2 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.1 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.8.0 nbconvert-7.8.0 nbformat-5.9.2 nbsphinx-0.9.3 numcodecs-0.11.0 numpy-1.25.2 pandas-2.0.3 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.10.0 prompt-toolkit-3.0.39 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.13.3 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2023.3 pyyaml-6.0.1 pyzmq-25.1.1 referencing-0.30.2 rpds-py-0.10.0 scanpydoc-0.9.5 scipy-1.11.2 soupsieve-2.4.1 sphinx-6.2.1 sphinx-autodoc-typehints-1.23.0 sphinx-book-theme-1.0.1 sphinx-copybutton-0.5.2 sphinx-issues-3.0.1 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxext-opengraph-0.8.2 stack-data-0.6.2 tinycss2-1.2.1 tornado-6.3.3 traitlets-5.9.0 typing-extensions-4.7.1 tzdata-2023.3 wcwidth-0.2.6 webencodings-0.5.1 zarr-2.16.1

[rtd-command-info] start-time: 2023-08-29T18:55:26.648233Z, end-time: 2023-08-29T18:55:26.704434Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
from pathlib import Path
from datetime import datetime
from importlib import metadata

from sphinx.application import Sphinx

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE / "extensions")]


# -- General configuration ------------------------------------------------


needs_sphinx = "1.7"  # autosummary bugfix

# General information
project = "anndata"
author = f"{project} developers"
copyright = f"{datetime.now():%Y}, {author}"
release = version = metadata.version("anndata")

# 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_copybutton",
    "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",  # needs to be before linkcode
    "sphinx.ext.linkcode",
    "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 = True


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 = "sphinx_book_theme"
html_theme_options = dict(
    use_repository_button=True,
    repository_url="https://github.com/scverse/anndata",
    repository_branch="main",
)
html_logo = "_static/img/anndata_schema.svg"
issues_github_path = "scverse/anndata"
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')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "latest",
    'version_slug': "latest",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("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': '',
    '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': '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': '22f33bb2',
}

# 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-anndata/builds/1690389/'

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: 2023-08-29T18:55:27.245338Z, end-time: 2023-08-29T18:57:17.584497Z, duration: 110, exit-code: 0
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v6.2.1
Matplotlib is building the font cache; this may take a moment.
making output directory... done
myst v2.0.0: 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/latest/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnLoader.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.IOSpec.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.iterate_axis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.AnnCollection.to_adata.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.IOSpec.encoding_type.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/generated/anndata.experimental.IOSpec.encoding_version.rst
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 39 source files that are out of date
updating environment: [new config] 113 added, 0 changed, 0 removed
reading sources... [  0%] _key_contributors
reading sources... [  1%] api
reading sources... [  2%] benchmark-read-write
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.11/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.5).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
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generating indices... genindex py-modindex done
copying linked files... 
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