Read the Docs build information
Build id: 221172
Project: icb-anndata
Version: latest
Commit: 2fef42a973b471e76c56b3d57ff0274c1935ac05
Date: 2019-07-05T05:48:07.091188Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-07-05T05:48:07.630395Z, end-time: 2019-07-05T05:48:07.641474Z, duration: 0, exit-code: 0
git remote set-url origin https://github.com/theislab/anndata.git


[rtd-command-info] start-time: 2019-07-05T05:48:07.722782Z, end-time: 2019-07-05T05:48:08.121056Z, duration: 0, exit-code: 0
git fetch --tags --prune --prune-tags --depth 50
From https://github.com/theislab/anndata
   19bd221..2fef42a  master     -> origin/master

[rtd-command-info] start-time: 2019-07-05T05:48:08.425211Z, end-time: 2019-07-05T05:48:08.461056Z, duration: 0, exit-code: 0
git checkout --force origin/master
Previous HEAD position was 19bd221 Merge pull request #172 from ivirshup/warn_flatten
HEAD is now at 2fef42a Allow asking for a key of obs when use_raw=True in deprecated _get_{obs,var}_array (#176)

[rtd-command-info] start-time: 2019-07-05T05:48:08.541612Z, end-time: 2019-07-05T05:48:08.553731Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-07-05T05:48:09.585858Z, end-time: 2019-07-05T05:48:15.474599Z, duration: 5, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python3.6
Not overwriting existing python script /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python (you must use /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python3.6)
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-07-05T05:48:15.568806Z, end-time: 2019-07-05T05:48:16.605206Z, duration: 1, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (19.1.1)

[rtd-command-info] start-time: 2019-07-05T05:48:16.692427Z, end-time: 2019-07-05T05:48:19.408053Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<0.6
Requirement already up-to-date: Pygments==2.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (2.3.1)
Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (41.0.1)
Requirement already up-to-date: docutils==0.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (0.14)
Requirement already up-to-date: mock==1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (1.0.1)
Requirement already up-to-date: pillow==5.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (5.4.1)
Requirement already up-to-date: alabaster!=0.7.5,<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (0.7.12)
Requirement already up-to-date: commonmark==0.8.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (0.8.1)
Requirement already up-to-date: recommonmark==0.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (0.5.0)
Requirement already up-to-date: sphinx<2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (1.8.5)
Requirement already up-to-date: sphinx-rtd-theme<0.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (0.4.3)
Requirement already up-to-date: readthedocs-sphinx-ext<0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (0.5.17)
Requirement already satisfied, skipping upgrade: future in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from commonmark==0.8.1) (0.17.1)
Requirement already satisfied, skipping upgrade: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.0)
Requirement already satisfied, skipping upgrade: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.9.0)
Requirement already satisfied, skipping upgrade: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.7.0)
Requirement already satisfied, skipping upgrade: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (19.0)
Requirement already satisfied, skipping upgrade: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.10.1)
Requirement already satisfied, skipping upgrade: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (2.22.0)
Requirement already satisfied, skipping upgrade: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.1.2)
Requirement already satisfied, skipping upgrade: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx<2) (1.12.0)
Requirement already satisfied, skipping upgrade: pytz>=2015.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from babel!=2.0,>=1.3->sphinx<2) (2019.1)
Requirement already satisfied, skipping upgrade: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx<2) (2.4.0)
Requirement already satisfied, skipping upgrade: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx<2) (1.1.1)
Requirement already satisfied, skipping upgrade: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (1.25.3)
Requirement already satisfied, skipping upgrade: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2.8)
Requirement already satisfied, skipping upgrade: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (2019.6.16)
Requirement already satisfied, skipping upgrade: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx<2) (3.0.4)

[rtd-command-info] start-time: 2019-07-05T05:48:19.498262Z, end-time: 2019-07-05T05:48:20.473442Z, duration: 0, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip -r docs/requires.txt
Requirement already satisfied: sphinx>=1.8 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 2)) (1.8.5)
Requirement already satisfied: sphinx-autodoc-typehints in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 3)) (1.6.0)
Requirement already satisfied: scanpydoc>=0.3.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 4)) (0.3.3)
Requirement already satisfied: pandas~=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 6)) (0.24.2)
Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 7)) (1.3.0)
Requirement already satisfied: h5py in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 8)) (2.9.0)
Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 9)) (6.0.0)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.10.1)
Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.22.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (0.7.12)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.3.1)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (19.0)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.1.2)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.7.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (41.0.1)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.9.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.1.0)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.12.0)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (0.14)
Requirement already satisfied: future-fstrings in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from scanpydoc>=0.3.2->-r docs/requires.txt (line 4)) (1.2.0)
Requirement already satisfied: get_version in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from scanpydoc>=0.3.2->-r docs/requires.txt (line 4)) (2.0.6)
Requirement already satisfied: pytz>=2011k in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 6)) (2019.1)
Requirement already satisfied: python-dateutil>=2.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 6)) (2.8.0)
Requirement already satisfied: numpy>=1.12.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from pandas~=0.21->-r docs/requires.txt (line 6)) (1.16.4)
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=1.8->-r docs/requires.txt (line 2)) (1.1.1)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx>=1.8->-r docs/requires.txt (line 2)) (1.25.3)
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Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=1.8->-r docs/requires.txt (line 2)) (2.4.0)

[rtd-command-info] start-time: 2019-07-05T05:48:21.187522Z, end-time: 2019-07-05T05:48:21.495777Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
import logging
from pathlib import Path
from datetime import datetime

HERE = Path(__file__).parent
sys.path.insert(0, str(HERE.parent))
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',
    # 'plot_generator',
    # 'plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    # 'ipython_directive',
    # 'ipython_console_highlighting',
    'scanpydoc',
]

# 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

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=('http://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),
)


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


html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=2,
)
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
)
html_static_path = ['_static']
html_show_sphinx = False

def setup(app):
    app.add_stylesheet('css/custom.css')


# -- 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
#


import importlib
import sys
import os.path
from six import string_types

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 mulitple 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://media.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://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-anndata/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-anndata',
    'name': u'anndata',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-anndata.readthedocs-hosted.com/en/stable/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    '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,
    'user_analytics_code': '',
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    'commit': '2fef42a9',
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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"]

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'),
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japanese = any([
    language_user == 'ja',
    project_language == 'ja',
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if chinese:
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    latex_elements_rtd = {
        'preamble': '\\usepackage[UTF8]{ctex}\n',
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    latex_elements = latex_elements_user or latex_elements_rtd
elif japanese:
    latex_engine = latex_engine_user or 'platex'

[rtd-command-info] start-time: 2019-07-05T05:48:21.641727Z, end-time: 2019-07-05T05:48:42.549265Z, duration: 20, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
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 http://pandas.pydata.org/pandas-docs/stable/objects.inv...
intersphinx inventory has moved: http://pandas.pydata.org/pandas-docs/stable/objects.inv -> 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...
[autosummary] generating autosummary for: api.rst, benchmarks.rst, index.rst, references.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.h5py.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.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isview.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.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.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.astype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.attrs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.chunks.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression_opts.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dims.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.external.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.file.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.fillvalue.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.id.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.create_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.append.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.value.rst
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release_notes.rst:43: WARNING: Title underline too short.

Version 0.4 :small:`December 23, 2017`
-------------------------------------
release_notes.rst:43: WARNING: Title underline too short.

Version 0.4 :small:`December 23, 2017`
-------------------------------------
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Version 0.4 :small:`December 23, 2017`
-------------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/release_notes.rst:43: WARNING: Title underline too short.

Version 0.4 :small:`December 23, 2017`
-------------------------------------
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generating indices... genindex py-modindex
writing additional pages... search
copying static files... done
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dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 52 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-07-05T05:48:42.787661Z, end-time: 2019-07-05T05:48:49.818335Z, duration: 7, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.8.5
loading translations [en]... done
making output directory...
loading pickled environment... done
[autosummary] generating autosummary for: api.rst, benchmarks.rst, index.rst, references.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.h5py.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.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.isview.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.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.write_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.astype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.attrs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.chunks.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.compression_opts.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dims.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.external.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.file.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Dataset.fillvalue.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.id.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.File.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.create_dataset.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.Group.keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.append.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.dtype.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.format_str.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.shape.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.h5py.SparseDataset.value.rst
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Version 0.4 :small:`December 23, 2017`
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Version 0.4 :small:`December 23, 2017`
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Version 0.4 :small:`December 23, 2017`
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Version 0.4 :small:`December 23, 2017`
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