Read the Docs build information
Build id: 838733
Project: icb-anndata
Version: 694
Commit: 137ee91249d89c095fdd3773ec6f1eeaf94e4ba6
Date: 2022-01-31T16:02:09.875948Z
State: finished
Success: False


[rtd-command-info] start-time: 2022-01-31T16:02:11.828642Z, end-time: 2022-01-31T16:02:12.980265Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-01-31T16:02:13.176992Z, end-time: 2022-01-31T16:02:13.828606Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/694/head:external-694
From https://github.com/theislab/anndata
 * [new ref]         refs/pull/694/head -> external-694

[rtd-command-info] start-time: 2022-01-31T16:02:14.091959Z, end-time: 2022-01-31T16:02:14.172263Z, duration: 0, exit-code: 0
git checkout --force 137ee91249d89c095fdd3773ec6f1eeaf94e4ba6
Note: checking out '137ee91249d89c095fdd3773ec6f1eeaf94e4ba6'.

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 performing another checkout.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:

  git checkout -b <new-branch-name>

HEAD is now at 137ee91 Initial draft of AnnData HTML repr

[rtd-command-info] start-time: 2022-01-31T16:02:14.490387Z, end-time: 2022-01-31T16:02:14.543626Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-01-31T16:02:15.593652Z, end-time: 2022-01-31T16:02:19.908192Z, duration: 4, exit-code: 0
python3.7 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.7.9'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2022-01-31T16:02:20.079411Z, end-time: 2022-01-31T16:02:23.194384Z, duration: 3, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip==21.3.1 setuptools<58.3.0
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Installing collected packages: setuptools, pip
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Successfully installed pip-21.3.1 setuptools-58.2.0

[rtd-command-info] start-time: 2022-01-31T16:02:23.446350Z, end-time: 2022-01-31T16:02:31.460883Z, duration: 8, 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
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Building wheels for collected packages: mock, future
  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=23773 sha256=ee63ab576fc764814c593540fa2c12ff14de3513362fa92675f4bf5f78b63f24
  Stored in directory: /tmp/pip-ephem-wheel-cache-s298ub1p/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
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  Stored in directory: /tmp/pip-ephem-wheel-cache-s298ub1p/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed Jinja2-3.0.3 MarkupSafe-2.0.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.11 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2021.3 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.27.1 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 urllib3-1.26.8
WARNING: You are using pip version 21.3.1; however, version 22.0.2 is available.
You should consider upgrading via the '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/bin/python -m pip install --upgrade pip' command.

[rtd-command-info] start-time: 2022-01-31T16:02:31.656799Z, end-time: 2022-01-31T16:03:11.885924Z, duration: 40, 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/694
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Building wheels for collected packages: anndata
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  Stored in directory: /tmp/pip-ephem-wheel-cache-60oor7qs/wheels/f6/7c/59/f46f80b584421d5cc034b9fea94416e19686d23616252df470
Successfully built anndata
Installing collected packages: zipp, typing-extensions, traitlets, pyrsistent, importlib-resources, importlib-metadata, attrs, tornado, pyzmq, python-dateutil, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, nbformat, jupyter-client, testpath, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, setuptools, pandocfilters, numpy, nbclient, mistune, jupyterlab-pygments, dunamai, defusedxml, cached-property, bleach, sphinx, scipy, pandas, nbconvert, natsort, h5py, get-version, sphinx-rtd-theme, sphinx-issues, sphinx-autodoc-typehints, scanpydoc, nbsphinx, anndata
  Attempting uninstall: setuptools
    Found existing installation: setuptools 58.2.0
    Uninstalling setuptools-58.2.0:
      Successfully uninstalled setuptools-58.2.0
  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 anndata-0.8.0rc2.dev1+g137ee91 attrs-21.4.0 bleach-4.1.0 cached-property-1.5.2 defusedxml-0.7.1 dunamai-1.8.0 entrypoints-0.3 get-version-3.5.3 h5py-3.6.0 importlib-metadata-4.10.1 importlib-resources-5.4.0 ipython-genutils-0.2.0 jsonschema-4.4.0 jupyter-client-7.1.2 jupyter-core-4.9.1 jupyterlab-pygments-0.1.2 mistune-0.8.4 natsort-8.1.0 nbclient-0.5.10 nbconvert-6.4.1 nbformat-5.1.3 nbsphinx-0.8.8 nest-asyncio-1.5.4 numpy-1.21.5 pandas-1.3.5 pandocfilters-1.5.0 pyrsistent-0.18.1 python-dateutil-2.8.2 pyzmq-22.3.0 scanpydoc-0.7.5 scipy-1.7.3 setuptools-60.6.0 sphinx-4.1.2 sphinx-autodoc-typehints-1.16.0 sphinx-issues-3.0.1 sphinx-rtd-theme-1.0.0 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 testpath-0.5.0 tornado-6.1 traitlets-5.1.1 typing-extensions-4.0.1 webencodings-0.5.1 zipp-3.7.0
WARNING: You are using pip version 21.3.1; however, version 22.0.2 is available.
You should consider upgrading via the '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/bin/python -m pip install --upgrade pip' command.

[rtd-command-info] start-time: 2022-01-31T16:03:13.312489Z, end-time: 2022-01-31T16:03:13.375350Z, 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")]
todo_include_todos = False
nitpicky = True  # Report broken links
nitpick_ignore = [
    ("py:meth", "pandas.DataFrame.iloc"),
    ("py:meth", "pandas.DataFrame.loc"),
]
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/reference/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
    zarr=("https://zarr.readthedocs.io/en/stable/", None),
    xarray=("http://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",
    # Temporarily
    "anndata._core.raw.Raw": "anndata.AnnData",
    "anndata._core.views.ArrayView": "numpy.ndarray",
    **{
        f"anndata._core.aligned_mapping.{cls}{kind}": "typing.Mapping"
        for cls in "Layers AxisArrays PairwiseArrays".split()
        for kind in ["", "View"]
    },
}

# -- Options for HTML output ----------------------------------------------


html_theme = "scanpydoc"
html_theme_options = dict(navigation_depth=4)
html_context = dict(
    display_github=True,  # Integrate GitHub
    github_user="theislab",  # 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/master/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': "694",
    'version_slug': "694",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("0.4.1", "/en/0.4.1/"),
    ("0.3", "/en/0.3/"),
    ("refpaths", "/en/refpaths/"),
    ],
    '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': 'theislab',
    'proxied_api_host': '/_',
    'github_repo': 'anndata',
    'github_version': '137ee91249d89c095fdd3773ec6f1eeaf94e4ba6',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '137ee91249d89c095fdd3773ec6f1eeaf94e4ba6',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '137ee91249d89c095fdd3773ec6f1eeaf94e4ba6',
    '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': '137ee912',
}

# 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/theislab/anndata/pull/694'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/838733/'

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: 2022-01-31T16:03:13.545483Z, end-time: 2022-01-31T16:03:26.121494Z, duration: 12, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.1.2
loading translations [en]... done
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/reference/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 http://xarray.pydata.org/en/stable/objects.inv...
intersphinx inventory has moved: http://xarray.pydata.org/en/stable/objects.inv -> https://xarray.pydata.org/en/stable/objects.inv
[autosummary] generating autosummary for: _key_contributors.rst, api.rst, benchmark-read-write.ipynb, benchmarks.rst, concatenation.rst, fileformat-prose.rst, index.rst, news.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnLoader.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.read_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.write_elem.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.convert.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.has_backed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.iterate_axis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.lazy_attr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.n_obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.n_vars.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.obs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.obsm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/docs/generated/anndata.experimental.AnnCollection.to_adata.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 12 source files that are out of date
updating environment: [new config] 81 added, 0 changed, 0 removed
reading sources... [  1%] _key_contributors
reading sources... [  2%] api
reading sources... [  3%] benchmark-read-write
reading sources... [  4%] benchmarks
reading sources... [  6%] concatenation
reading sources... [  7%] fileformat-prose
reading sources... [  8%] generated/anndata.AnnData
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reading sources... [ 16%] generated/anndata.AnnData.copy
reading sources... [ 17%] generated/anndata.AnnData.filename
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reading sources... [ 35%] generated/anndata.AnnData.rename_categories
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reading sources... [ 38%] generated/anndata.AnnData.strings_to_categoricals
reading sources... [ 39%] generated/anndata.AnnData.to_df
reading sources... [ 40%] generated/anndata.AnnData.to_memory
reading sources... [ 41%] generated/anndata.AnnData.transpose
reading sources... [ 43%] generated/anndata.AnnData.uns
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reading sources... [ 55%] generated/anndata.AnnData.write
reading sources... [ 56%] generated/anndata.AnnData.write_csvs
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looking for now-outdated files... none found
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/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/anndata/experimental/pytorch/_annloader.py:18: UserWarning: Сould not load pytorch.
  warnings.warn("Сould not load pytorch.")

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/cmd/build.py", line 280, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/application.py", line 343, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 295, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 357, in build
    self.write(docnames, list(updated_docnames), method)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 531, in write
    self._write_serial(sorted(docnames))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/builders/__init__.py", line 541, in _write_serial
    self.write_doc(docname, doctree)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/contextlib.py", line 119, in __exit__
    next(self.gen)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/util/logging.py", line 213, in pending_warnings
    memhandler.flushTo(logger)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/util/logging.py", line 178, in flushTo
    logger.handle(record)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/logging/__init__.py", line 1524, in handle
    self.callHandlers(record)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/logging/__init__.py", line 1586, in callHandlers
    hdlr.handle(record)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/logging/__init__.py", line 890, in handle
    rv = self.filter(record)
  File "/home/docs/.pyenv/versions/3.7.9/lib/python3.7/logging/__init__.py", line 751, in filter
    result = f.filter(record)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/694/lib/python3.7/site-packages/sphinx/util/logging.py", line 423, in filter
    raise exc
sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/anndata/_io/specs/registry.py:docstring of anndata._io.specs.registry.write_elem:3:py:class reference target not found: anndata.compat.ZarrGroup

Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/694/anndata/_io/specs/registry.py:docstring of anndata._io.specs.registry.write_elem:3:py:class reference target not found: anndata.compat.ZarrGroup