Read the Docs build information
Build id: 598927
Project: icb-anndata
Version: 527
Commit: 08239c22b0d6b3c38afd779abfe9539a7244fc02
Date: 2021-03-24T22:33:27.717197Z
State: finished
Success: True


[rtd-command-info] start-time: 2021-03-24T22:34:22.807135Z, end-time: 2021-03-24T22:34:23.675574Z, 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: 2021-03-24T22:34:34.849942Z, end-time: 2021-03-24T22:34:35.488137Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/527/head:external-527
From https://github.com/theislab/anndata
 * [new ref]         refs/pull/527/head -> external-527

[rtd-command-info] start-time: 2021-03-24T22:34:35.638968Z, end-time: 2021-03-24T22:34:35.718068Z, duration: 0, exit-code: 0
git checkout --force 08239c22b0d6b3c38afd779abfe9539a7244fc02
Note: checking out '08239c22b0d6b3c38afd779abfe9539a7244fc02'.

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 08239c2 Also handle dense .X, and backed, in sum_by()

[rtd-command-info] start-time: 2021-03-24T22:34:35.845438Z, end-time: 2021-03-24T22:34:35.917751Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2021-03-24T22:34:41.856161Z, end-time: 2021-03-24T22:34:56.511683Z, duration: 14, exit-code: 0
python3.6 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.6.12'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/527/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/527/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2021-03-24T22:34:56.632999Z, end-time: 2021-03-24T22:34:58.469799Z, 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/527/lib/python3.6/site-packages (21.0.1)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/527/lib/python3.6/site-packages (54.2.0)

[rtd-command-info] start-time: 2021-03-24T22:34:58.588986Z, end-time: 2021-03-24T22:35:08.010388Z, duration: 9, 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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Building wheels for collected packages: mock, future
  Building wheel for mock (setup.py): started
  Building wheel for mock (setup.py): finished with status 'done'
  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23755 sha256=78218708461514663261dc8b3e56c85536242860a74c131f42bb22c3677513d2
  Stored in directory: /tmp/pip-ephem-wheel-cache-d3szoqyd/wheels/98/4d/ec/1aa935d28cb63b7b16037fc990302a34244ac3b0601a4e0c00
  Building wheel for future (setup.py): started
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  Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491059 sha256=1fa377a049793ad9ee579a7a04b7c20d4f97b8912ce74bbaf0c22c0f4429997c
  Stored in directory: /tmp/pip-ephem-wheel-cache-d3szoqyd/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
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-2.8.1 alabaster-0.7.12 babel-2.9.0 certifi-2020.12.5 chardet-4.0.0 commonmark-0.8.1 docutils-0.16 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-1.15.0 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: 2021-03-24T22:35:08.138814Z, end-time: 2021-03-24T22:35:37.973873Z, duration: 29, 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/527
  Installing build dependencies: started
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  Getting requirements to build wheel: started
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    Preparing wheel metadata: started
    Preparing wheel metadata: finished with status 'done'
Collecting natsort
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Requirement already satisfied: packaging>=20 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/527/lib/python3.6/site-packages (from anndata==0.1.dev50+g08239c2) (20.9)
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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-0.1.dev50+g08239c2-py3-none-any.whl size=124015 sha256=44cc396791e78d0649c4f9e44e7da3e6af011da2f4dbad2a699ed94c1e02e6e0
  Stored in directory: /tmp/pip-ephem-wheel-cache-_3dg4u2y/wheels/f1/bc/8e/490ab82a72153f0c186d03901a7c43fa254d41c08e6230369d
Successfully built anndata
Installing collected packages: zipp, typing-extensions, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, python-dateutil, numpy, cached-property, xlrd, sphinx, scipy, pandas, natsort, importlib-metadata, h5py, get-version, sphinx-rtd-theme, sphinx-issues, sphinx-autodoc-typehints, scanpydoc, anndata
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  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-0.1.dev50+g08239c2 cached-property-1.5.2 get-version-2.1 h5py-3.1.0 importlib-metadata-3.7.3 natsort-7.1.1 numpy-1.19.5 pandas-1.1.5 python-dateutil-2.8.1 scanpydoc-0.5.5 scipy-1.5.4 sphinx-3.5.3 sphinx-autodoc-typehints-1.11.1 sphinx-issues-1.2.0 sphinx-rtd-theme-0.5.1 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-3.7.4.3 xlrd-1.2.0 zipp-3.4.1

[rtd-command-info] start-time: 2021-03-24T22:35:39.322238Z, end-time: 2021-03-24T22:35:39.428719Z, 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 work_around_issue_6785():
    """See https://github.com/sphinx-doc/sphinx/issues/6785"""
    from docutils.parsers.rst import directives
    from sphinx.ext import autodoc
    from sphinx.domains.python import PyAttribute

    # check if the code changes on the sphinx side and we can remove this
    assert autodoc.PropertyDocumenter.directivetype == "method"
    autodoc.PropertyDocumenter.directivetype = "attribute"

    def get_signature_prefix(self, sig: str) -> str:
        # TODO: abstract attributes
        return "property " if "property" in self.options else ""

    PyAttribute.option_spec["property"] = directives.flag
    PyAttribute.get_signature_prefix = get_signature_prefix


def setup(app: Sphinx):
    work_around_issue_6785()
    # 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': "527",
    'version_slug': "527",
    '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': '08239c22b0d6b3c38afd779abfe9539a7244fc02',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '08239c22b0d6b3c38afd779abfe9539a7244fc02',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '08239c22b0d6b3c38afd779abfe9539a7244fc02',
    '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': '08239c22',
}

# 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/527'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/598927/'

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: 2021-03-24T22:35:39.560523Z, end-time: 2021-03-24T22:35:50.754586Z, duration: 11, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v3.5.3
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: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/stable/objects.inv
intersphinx inventory has moved: http://docs.h5py.org/en/latest/objects.inv -> https://docs.h5py.org/en/latest/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/527/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.ImplicitModificationWarning.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.concat.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.layers.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/527/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] 65 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... [ 13%] anndata.AnnData.filename
reading sources... [ 15%] anndata.AnnData.is_view
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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... [ 24%] anndata.AnnData.obs_keys
reading sources... [ 26%] anndata.AnnData.obs_names
reading sources... [ 27%] anndata.AnnData.obs_names_make_unique
reading sources... [ 29%] anndata.AnnData.obs_vector
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reading sources... [ 32%] anndata.AnnData.obsm_keys
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reading sources... [ 40%] anndata.AnnData.strings_to_categoricals
reading sources... [ 41%] anndata.AnnData.sum_by
reading sources... [ 43%] anndata.AnnData.to_df
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reading sources... [ 70%] anndata.ImplicitModificationWarning
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reading sources... [ 73%] anndata.read_csv
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reading sources... [ 87%] api
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reading sources... [ 90%] concatenation
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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
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writing output... [ 40%] anndata.AnnData.strings_to_categoricals
writing output... [ 41%] anndata.AnnData.sum_by
writing output... [ 43%] anndata.AnnData.to_df
writing output... [ 44%] anndata.AnnData.to_memory
writing output... [ 46%] anndata.AnnData.transpose
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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...