Read the Docs build information
Build id: 631086
Project: icb-anndata
Version: latest
Commit: 31e4eedd4f34e0db9d859aa422950b9d957bc202
Date: 2021-05-11T19:39:07.751987Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-05-11T19:39:09.174963Z, end-time: 2021-05-11T19:39:10.083773Z, duration: 0, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2021-05-11T19:39:10.242505Z, end-time: 2021-05-11T19:39:10.318054Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

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 31e4eed Update CI (#562)

[rtd-command-info] start-time: 2021-05-11T19:39:10.445302Z, end-time: 2021-05-11T19:39:10.516156Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-05-11T19:39:11.490007Z, end-time: 2021-05-11T19:39:15.501737Z, 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/latest/bin/python3.7
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-05-11T19:39:15.629469Z, end-time: 2021-05-11T19:39:16.741630Z, duration: 1, 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/python3.7/site-packages (21.1.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.7/site-packages (56.2.0)

[rtd-command-info] start-time: 2021-05-11T19:39:16.846514Z, end-time: 2021-05-11T19:39:25.032513Z, 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
Collecting mock==1.0.1
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Collecting pillow==5.4.1
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.7/site-packages (from sphinx<2) (56.2.0)
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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=23755 sha256=9fba133b6f234bb71de6a5a63d914b1d7d1cbc96ca9944a96b0efdc5dcd07921
  Stored in directory: /tmp/pip-ephem-wheel-cache-_hrqagge/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1
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  Stored in directory: /tmp/pip-ephem-wheel-cache-_hrqagge/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, chardet, 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 Jinja2-2.11.3 MarkupSafe-1.1.1 Pygments-2.9.0 alabaster-0.7.12 babel-2.9.1 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-2.10 imagesize-1.2.0 mock-1.0.1 packaging-20.9 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.25.1 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.4 sphinxcontrib-websupport-1.2.4 urllib3-1.26.4

[rtd-command-info] start-time: 2021-05-11T19:39:25.145346Z, end-time: 2021-05-11T19:39:57.735158Z, duration: 32, 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/latest
  DEPRECATION: A future pip version will change local packages to be built in-place without first copying to a temporary directory. We recommend you use --use-feature=in-tree-build to test your packages with this new behavior before it becomes the default.
   pip 21.3 will remove support for this functionality. You can find discussion regarding this at https://github.com/pypa/pip/issues/7555.
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
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  Installing backend dependencies: started
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    Preparing wheel metadata: started
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Collecting scipy>1.4
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Requirement already satisfied: packaging>=20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.7/site-packages (from anndata==0.7.7.dev1+g31e4eed) (20.9)
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Collecting get_version
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Collecting cached-property
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Building wheels for collected packages: anndata
  Building wheel for anndata (PEP 517): started
  Building wheel for anndata (PEP 517): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.7.7.dev1+g31e4eed-py3-none-any.whl size=127758 sha256=08f88af3d53db917bb520584b77fcf607835d987fef83cb64941ed24985c30b0
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Successfully built anndata
Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, python-dateutil, numpy, docutils, cached-property, xlrd, sphinx, scipy, pandas, natsort, importlib-metadata, h5py, get-version, sphinx-rtd-theme, sphinx-issues, sphinx-autodoc-typehints, scanpydoc, anndata
  Attempting uninstall: docutils
    Found existing installation: docutils 0.17.1
    Uninstalling docutils-0.17.1:
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  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
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  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-0.7.7.dev1+g31e4eed cached-property-1.5.2 docutils-0.16 get-version-2.2 h5py-3.2.1 importlib-metadata-4.0.1 natsort-7.1.1 numpy-1.20.3 pandas-1.2.4 python-dateutil-2.8.1 scanpydoc-0.7.1 scipy-1.6.3 sphinx-4.0.1 sphinx-autodoc-typehints-1.12.0 sphinx-issues-1.2.0 sphinx-rtd-theme-0.5.2 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-1.0.3 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 typing-extensions-3.10.0.0 xlrd-1.2.0 zipp-3.4.1

[rtd-command-info] start-time: 2021-05-11T19:39:58.600020Z, end-time: 2021-05-11T19:39:58.670923Z, 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 = anndata.__author__
copyright = f"{datetime.now():%Y}, {author}."
version = anndata.__version__.replace(".dirty", "")
release = version

# default settings
templates_path = ["_templates"]
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",
    *[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
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=("http://docs.h5py.org/en/latest/", None),
    loompy=("https://linnarssonlab.org/loompy/", None),
    numpy=("https://docs.scipy.org/doc/numpy/", 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 = {
    "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 should't rely on extra depencies.

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': "latest",
    'version_slug': "latest",
    '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': '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': '31e4eedd',
}

# 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 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/631086/'

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: 2021-05-11T19:39:58.780512Z, end-time: 2021-05-11T19:40:07.622130Z, duration: 8, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v4.0.1
loading translations [en]... done
making output directory... done
loading intersphinx inventory from http://docs.h5py.org/en/latest/objects.inv...
loading intersphinx inventory from https://linnarssonlab.org/loompy/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/numpy/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://docs.h5py.org/en/latest/objects.inv -> https://docs.h5py.org/en/latest/objects.inv
intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv
[autosummary] generating autosummary for: _key_contributors.rst, api.rst, benchmarks.rst, concatenation.rst, fileformat-prose.rst, index.rst, news.rst, references.rst, release-latest.rst, release-notes.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.write_zarr.rst
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 10 source files that are out of date
updating environment: [new config] 64 added, 0 changed, 0 removed
reading sources... [  1%] _key_contributors
reading sources... [  3%] anndata.AnnData
reading sources... [  4%] anndata.AnnData.T
reading sources... [  6%] anndata.AnnData.X
reading sources... [  7%] anndata.AnnData.chunk_X
reading sources... [  9%] anndata.AnnData.chunked_X
reading sources... [ 10%] anndata.AnnData.concatenate
reading sources... [ 12%] anndata.AnnData.copy
reading sources... [ 14%] anndata.AnnData.filename
reading sources... [ 15%] anndata.AnnData.is_view
reading sources... [ 17%] anndata.AnnData.isbacked
reading sources... [ 18%] anndata.AnnData.layers
reading sources... [ 20%] anndata.AnnData.n_obs
reading sources... [ 21%] anndata.AnnData.n_vars
reading sources... [ 23%] anndata.AnnData.obs
reading sources... [ 25%] anndata.AnnData.obs_keys
reading sources... [ 26%] anndata.AnnData.obs_names
reading sources... [ 28%] anndata.AnnData.obs_names_make_unique
reading sources... [ 29%] anndata.AnnData.obs_vector
reading sources... [ 31%] anndata.AnnData.obsm
reading sources... [ 32%] anndata.AnnData.obsm_keys
reading sources... [ 34%] anndata.AnnData.obsp
reading sources... [ 35%] anndata.AnnData.raw
reading sources... [ 37%] anndata.AnnData.rename_categories
reading sources... [ 39%] anndata.AnnData.shape
reading sources... [ 40%] anndata.AnnData.strings_to_categoricals
reading sources... [ 42%] anndata.AnnData.to_df
reading sources... [ 43%] anndata.AnnData.to_memory
reading sources... [ 45%] anndata.AnnData.transpose
reading sources... [ 46%] anndata.AnnData.uns
reading sources... [ 48%] anndata.AnnData.uns_keys
reading sources... [ 50%] anndata.AnnData.var
reading sources... [ 51%] anndata.AnnData.var_keys
reading sources... [ 53%] anndata.AnnData.var_names
reading sources... [ 54%] anndata.AnnData.var_names_make_unique
reading sources... [ 56%] anndata.AnnData.var_vector
reading sources... [ 57%] anndata.AnnData.varm
reading sources... [ 59%] anndata.AnnData.varm_keys
reading sources... [ 60%] anndata.AnnData.varp
reading sources... [ 62%] anndata.AnnData.write
reading sources... [ 64%] anndata.AnnData.write_csvs
reading sources... [ 65%] anndata.AnnData.write_h5ad
reading sources... [ 67%] anndata.AnnData.write_loom
reading sources... [ 68%] anndata.AnnData.write_zarr
reading sources... [ 70%] anndata.ImplicitModificationWarning
reading sources... [ 71%] anndata.concat
reading sources... [ 73%] anndata.read_csv
reading sources... [ 75%] anndata.read_excel
reading sources... [ 76%] anndata.read_h5ad
reading sources... [ 78%] anndata.read_hdf
reading sources... [ 79%] anndata.read_loom
reading sources... [ 81%] anndata.read_mtx
reading sources... [ 82%] anndata.read_text
reading sources... [ 84%] anndata.read_umi_tools
reading sources... [ 85%] anndata.read_zarr
reading sources... [ 87%] api
reading sources... [ 89%] benchmarks
reading sources... [ 90%] concatenation
reading sources... [ 92%] fileformat-prose
reading sources... [ 93%] index
reading sources... [ 95%] news
reading sources... [ 96%] references
reading sources... [ 98%] release-latest
reading sources... [100%] release-notes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  1%] _key_contributors
writing output... [  3%] anndata.AnnData
writing output... [  4%] anndata.AnnData.T
writing output... [  6%] anndata.AnnData.X
writing output... [  7%] anndata.AnnData.chunk_X
writing output... [  9%] anndata.AnnData.chunked_X
writing output... [ 10%] anndata.AnnData.concatenate
writing output... [ 12%] anndata.AnnData.copy
writing output... [ 14%] anndata.AnnData.filename
writing output... [ 15%] anndata.AnnData.is_view
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writing output... [ 18%] anndata.AnnData.layers
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writing output... [ 25%] anndata.AnnData.obs_keys
writing output... [ 26%] anndata.AnnData.obs_names
writing output... [ 28%] anndata.AnnData.obs_names_make_unique
writing output... [ 29%] anndata.AnnData.obs_vector
writing output... [ 31%] anndata.AnnData.obsm
writing output... [ 32%] anndata.AnnData.obsm_keys
writing output... [ 34%] anndata.AnnData.obsp
writing output... [ 35%] anndata.AnnData.raw
writing output... [ 37%] anndata.AnnData.rename_categories
writing output... [ 39%] anndata.AnnData.shape
writing output... [ 40%] anndata.AnnData.strings_to_categoricals
writing output... [ 42%] anndata.AnnData.to_df
writing output... [ 43%] anndata.AnnData.to_memory
writing output... [ 45%] anndata.AnnData.transpose
writing output... [ 46%] anndata.AnnData.uns
writing output... [ 48%] anndata.AnnData.uns_keys
writing output... [ 50%] anndata.AnnData.var
writing output... [ 51%] anndata.AnnData.var_keys
writing output... [ 53%] anndata.AnnData.var_names
writing output... [ 54%] anndata.AnnData.var_names_make_unique
writing output... [ 56%] anndata.AnnData.var_vector
writing output... [ 57%] anndata.AnnData.varm
writing output... [ 59%] anndata.AnnData.varm_keys
writing output... [ 60%] anndata.AnnData.varp
writing output... [ 62%] anndata.AnnData.write
writing output... [ 64%] anndata.AnnData.write_csvs
writing output... [ 65%] anndata.AnnData.write_h5ad
writing output... [ 67%] anndata.AnnData.write_loom
writing output... [ 68%] anndata.AnnData.write_zarr
writing output... [ 70%] anndata.ImplicitModificationWarning
writing output... [ 71%] anndata.concat
writing output... [ 73%] anndata.read_csv
writing output... [ 75%] anndata.read_excel
writing output... [ 76%] anndata.read_h5ad
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writing output... [ 79%] anndata.read_loom
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writing output... [ 82%] anndata.read_text
writing output... [ 84%] anndata.read_umi_tools
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writing output... [ 87%] api
writing output... [ 89%] benchmarks
writing output... [ 90%] concatenation
writing output... [ 92%] fileformat-prose
writing output... [ 93%] index
writing output... [ 95%] news
writing output... [ 96%] references
writing output... [ 98%] release-latest
writing output... [100%] release-notes

generating indices... genindex py-modindex done
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in _build/html.
Updating searchtools for Read the Docs search...