Read the Docs build information
Build id: 1647417
Project: icb-anndata
Version: 947
Commit: 9d53307efc00489779f77528d9d7ab315854d5ea
Date: 2023-08-08T11:42:50.565539Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-08-08T11:42:54.676285Z, end-time: 2023-08-08T11:42:55.807645Z, 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: 2023-08-08T11:42:56.314902Z, end-time: 2023-08-08T11:42:56.923725Z, 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: 2023-08-08T11:42:57.133162Z, end-time: 2023-08-08T11:42:57.224445Z, duration: 0, exit-code: 0
git checkout --force 9d53307efc00489779f77528d9d7ab315854d5ea
Note: switching to '9d53307efc00489779f77528d9d7ab315854d5ea'.

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 9d53307 (style): change folder structure

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git clean -d -f -f


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git submodule sync


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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'

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cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: "3.10"
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: 2023-08-08T11:43:05.872513Z, end-time: 2023-08-08T11:43:05.945691Z, duration: 0, exit-code: 0
asdf global python 3.10.12


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.10.12.final.0-64 in 662ms
  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

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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/947/lib/python3.10/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/947/lib/python3.10/site-packages (57.4.0)
Collecting setuptools
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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-68.0.0

[rtd-command-info] start-time: 2023-08-08T11:43:21.026719Z, end-time: 2023-08-08T11:43:29.072332Z, duration: 8, 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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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=f2cfe5f9b6cebaa21c159a8ff8768aa5218d533920780d0e7d99131ebbbd3f76
  Stored in directory: /tmp/pip-ephem-wheel-cache-v9kls9u3/wheels/df/9a/50/99d488b71fc0b027f0d316f4e447cdc9b973c67e1e7e4abc4b
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: 2023-08-08T11:43:29.370396Z, end-time: 2023-08-08T11:44:05.070959Z, duration: 35, 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/947
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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-0.10.0.dev147+g9d53307-py3-none-any.whl size=122499 sha256=fa59ff3af5fa3e3ff3317800f333830443b9713c18dbb4d65647867795dd57b2
  Stored in directory: /tmp/pip-ephem-wheel-cache-lp1q32o8/wheels/7b/50/aa/b1ccb798365611f213b22186672a3b613605f0e618fdde3165
  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=993d17fd81979cf9ae810ed7cb9c9517647902c914aa3d5642ea49bff75184e6
  Stored in directory: /tmp/pip-ephem-wheel-cache-lp1q32o8/wheels/7f/4e/be/1171b40f43b918087657ec57cf3b81fa1a2e027d8755baa184
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-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, 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, sphinx, scipy, referencing, pandas, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, h5py, contourpy, beautifulsoup4, awkward-cpp, zarr, sphinx-issues, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, ipython, awkward, anndata, sphinxext-opengraph, sphinx-book-theme, myst-parser, jsonschema, nbformat, nbclient, nbconvert, nbsphinx
  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-0.10.0.dev147+g9d53307 array-api-compat-1.3 asciitree-0.3.3 asttokens-2.2.1 attrs-23.1.0 awkward-2.3.1 awkward-cpp-21 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-4.42.0 h5py-3.9.0 ipython-8.14.0 jedi-0.19.0 jsonschema-4.19.0 jsonschema-specifications-2023.7.1 jupyter-client-8.3.0 jupyter-core-5.3.1 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 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-7.7.3 nbformat-5.9.2 nbsphinx-0.9.2 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-25.1.0 referencing-0.30.2 rpds-py-0.9.2 scanpydoc-0.9.4 scipy-1.11.1 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-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext-opengraph-0.8.2 stack-data-0.6.2 tinycss2-1.2.1 tornado-6.3.2 traitlets-5.9.0 typing-extensions-4.7.1 tzdata-2023.3 wcwidth-0.2.6 webencodings-0.5.1 zarr-2.16.0

[rtd-command-info] start-time: 2023-08-08T11:44:08.085221Z, end-time: 2023-08-08T11:44:08.142363Z, 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')

# 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': '',
    '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': '9d53307efc00489779f77528d9d7ab315854d5ea',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '9d53307efc00489779f77528d9d7ab315854d5ea',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '9d53307efc00489779f77528d9d7ab315854d5ea',
    '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': '9d53307e',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





if 'html_context' in globals():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
else:
    html_context = context

# Add custom RTD extension
if 'extensions' in globals():
    # Insert at the beginning because it can interfere
    # with other extensions.
    # See https://github.com/rtfd/readthedocs.org/pull/4054
    extensions.insert(0, "readthedocs_ext.readthedocs")
else:
    extensions = ["readthedocs_ext.readthedocs"]

# Add External version warning banner to the external version documentation
if 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/anndata/pull/947'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/1647417/'

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: 2023-08-08T11:44:08.436063Z, end-time: 2023-08-08T11:44:19.528073Z, duration: 11, exit-code: 2
python -m sphinx -T -E -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v6.2.1
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...
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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

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/ext/autosummary/generate.py", line 455, in generate_autosummary_docs
    name, obj, parent, modname = import_by_name(entry.name)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/ext/autosummary/__init__.py", line 659, in import_by_name
    raise ImportExceptionGroup('no module named %s' % ' or '.join(tried), exceptions)
sphinx.ext.autosummary.ImportExceptionGroup: no module named anndata.AnnData

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/events.py", line 96, in emit
    results.append(listener.handler(self.app, *args))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/ext/autosummary/__init__.py", line 818, in process_generate_options
    generate_autosummary_docs(genfiles, suffix=suffix, base_path=app.srcdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/ext/autosummary/generate.py", line 460, in generate_autosummary_docs
    name, obj, parent, modname = import_ivar_by_name(entry.name)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/ext/autosummary/__init__.py", line 717, in import_ivar_by_name
    real_name, obj, parent, modname = import_by_name(name, prefixes, grouped_exception)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/ext/autosummary/__init__.py", line 659, in import_by_name
    raise ImportExceptionGroup('no module named %s' % ' or '.join(tried), exceptions)
sphinx.ext.autosummary.ImportExceptionGroup: no module named anndata

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/application.py", line 268, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/application.py", line 341, in _init_builder
    self.events.emit('builder-inited')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages/sphinx/events.py", line 107, in emit
    raise ExtensionError(__("Handler %r for event %r threw an exception") %
sphinx.errors.ExtensionError: Handler <function process_generate_options at 0x7f31bc0bc280> for event 'builder-inited' threw an exception (exception: no module named anndata)

Extension error (sphinx.ext.autosummary):
Handler <function process_generate_options at 0x7f31bc0bc280> for event 'builder-inited' threw an exception (exception: no module named anndata)