Read the Docs build information
Build id: 280252
Project: icb-anndata
Version: stable
Commit: ff995f1c4df7acd1b012a6c16afd7b513d89b3c2
Date: 2020-01-24T17:40:31.034311Z
State: finished
Success: True


[rtd-command-info] start-time: 2020-01-24T17:41:34.409436Z, end-time: 2020-01-24T17:41:35.721039Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-01-24T17:41:36.063539Z, end-time: 2020-01-24T17:41:36.283606Z, duration: 0, exit-code: 0
git checkout --force origin/stable
Note: checking out 'origin/stable'.

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 ff995f1 Circumvent sphinx-doc/sphinx/6785 (#307)

[rtd-command-info] start-time: 2020-01-24T17:41:36.457209Z, end-time: 2020-01-24T17:41:36.686332Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-01-24T17:41:38.091616Z, end-time: 2020-01-24T17:41:42.657042Z, duration: 4, 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/stable/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-01-24T17:41:42.761354Z, end-time: 2020-01-24T17:41:45.271229Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip pip
Collecting pip
  Downloading https://files.pythonhosted.org/packages/54/0c/d01aa759fdc501a58f431eb594a17495f15b88da142ce14b5845662c13f3/pip-20.0.2-py2.py3-none-any.whl (1.4MB)
Installing collected packages: pip
  Found existing installation: pip 19.1.1
    Uninstalling pip-19.1.1:
      Successfully uninstalled pip-19.1.1
Successfully installed pip-20.0.2

[rtd-command-info] start-time: 2020-01-24T17:41:45.347024Z, end-time: 2020-01-24T17:41:56.225383Z, duration: 10, 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<1.1
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Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages (41.0.1)
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Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, pytz, babel, imagesize, six, pyparsing, packaging, sphinxcontrib-websupport, chardet, idna, certifi, urllib3, requests, MarkupSafe, Jinja2, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.10.3 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.8 imagesize-1.2.0 mock-1.0.1 packaging-20.1 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.22.0 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.8

[rtd-command-info] start-time: 2020-01-24T17:41:56.309001Z, end-time: 2020-01-24T17:42:17.091814Z, duration: 20, 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
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Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/b3/3a/6e/c2cd6df1849363f3d56ba11e64368aa1ef3ac886f39c765e82/zarr-2.4.0-py3-none-any.whl
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Installing collected packages: setuptools-scm, more-itertools, zipp, importlib-metadata, typing-extensions, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, sphinx-issues, python-dateutil, numpy, pandas, scipy, h5py, natsort, monotonic, fasteners, numcodecs, asciitree, zarr
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Successfully installed asciitree-0.3.3 fasteners-0.15 get-version-2.1 h5py-2.10.0 importlib-metadata-1.4.0 monotonic-1.5 more-itertools-8.1.0 natsort-7.0.0 numcodecs-0.6.4 numpy-1.18.1 pandas-0.25.3 python-dateutil-2.8.1 scanpydoc-0.4.5 scipy-1.4.1 setuptools-scm-3.4.3 sphinx-2.3.1 sphinx-autodoc-typehints-1.10.3 sphinx-issues-1.2.0 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 typing-extensions-3.7.4.1 zarr-2.4.0 zipp-2.0.1

[rtd-command-info] start-time: 2020-01-24T17:42:17.860002Z, end-time: 2020-01-24T17:42:18.076497Z, 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
    "sphinx_issues",
    # "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
suppress_warnings = ["ref.citation"]


def work_around_issue_6785():
    """See https://github.com/sphinx-doc/sphinx/issues/6785"""
    from sphinx.ext import autodoc

    # check if the code changes on the sphinx side and we can remove this
    assert autodoc.PropertyDocumenter.priority > autodoc.AttributeDocumenter.priority
    autodoc.PropertyDocumenter.priority = -100


def setup(app):
    work_around_issue_6785()
    # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead.
    app.warningiserror = True
    app.add_stylesheet("css/custom.css")


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),
)
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 = "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
)
issues_github_path = "{github_user}/{github_repo}".format_map(html_context)
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 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://media.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "stable",
    'version_slug': "stable",
    '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", "//icb-anndata.readthedocs-hosted.com/_/downloads/en/stable/htmlzip/"),
    ],
    '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',
    'proxied_api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    'github_repo': 'anndata',
    'github_version': 'stable',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'stable',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'stable',
    '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': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'ff995f1c',
}




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")

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'

[rtd-command-info] start-time: 2020-01-24T17:42:18.152517Z, end-time: 2020-01-24T17:42:31.473871Z, duration: 13, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.3.1
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...
[autosummary] generating autosummary for: api.rst, benchmarks.rst, fileformat-prose.rst, index.rst, references.rst, release_notes.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isview.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_h5ad.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 6 source files that are out of date
updating environment: [new config] 58 added, 0 changed, 0 removed
reading sources... [  1%] anndata.AnnData
reading sources... [  3%] anndata.AnnData.T
reading sources... [  5%] anndata.AnnData.X
reading sources... [  6%] anndata.AnnData.chunk_X
reading sources... [  8%] 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
reading sources... [ 17%] anndata.AnnData.isbacked
reading sources... [ 18%] anndata.AnnData.isview
reading sources... [ 20%] anndata.AnnData.layers
reading sources... [ 22%] anndata.AnnData.n_obs
reading sources... [ 24%] anndata.AnnData.n_vars
reading sources... [ 25%] anndata.AnnData.obs
reading sources... [ 27%] anndata.AnnData.obs_keys
reading sources... [ 29%] anndata.AnnData.obs_names
reading sources... [ 31%] anndata.AnnData.obs_names_make_unique
reading sources... [ 32%] anndata.AnnData.obs_vector
reading sources... [ 34%] anndata.AnnData.obsm
reading sources... [ 36%] anndata.AnnData.obsm_keys
reading sources... [ 37%] anndata.AnnData.obsp
reading sources... [ 39%] anndata.AnnData.raw
reading sources... [ 41%] anndata.AnnData.rename_categories
reading sources... [ 43%] anndata.AnnData.shape
reading sources... [ 44%] anndata.AnnData.strings_to_categoricals
reading sources... [ 46%] anndata.AnnData.to_df
reading sources... [ 48%] anndata.AnnData.transpose
reading sources... [ 50%] anndata.AnnData.uns
reading sources... [ 51%] anndata.AnnData.uns_keys
reading sources... [ 53%] anndata.AnnData.var
reading sources... [ 55%] anndata.AnnData.var_keys
reading sources... [ 56%] anndata.AnnData.var_names
reading sources... [ 58%] anndata.AnnData.var_names_make_unique
reading sources... [ 60%] anndata.AnnData.var_vector
reading sources... [ 62%] anndata.AnnData.varm
reading sources... [ 63%] anndata.AnnData.varm_keys
reading sources... [ 65%] anndata.AnnData.varp
reading sources... [ 67%] anndata.AnnData.write
reading sources... [ 68%] anndata.AnnData.write_csvs
reading sources... [ 70%] anndata.AnnData.write_h5ad
reading sources... [ 72%] anndata.AnnData.write_loom
reading sources... [ 74%] anndata.AnnData.write_zarr
reading sources... [ 75%] anndata.read_csv
reading sources... [ 77%] anndata.read_excel
reading sources... [ 79%] anndata.read_h5ad
reading sources... [ 81%] anndata.read_hdf
reading sources... [ 82%] anndata.read_loom
reading sources... [ 84%] anndata.read_mtx
reading sources... [ 86%] anndata.read_text
reading sources... [ 87%] anndata.read_umi_tools
reading sources... [ 89%] anndata.read_zarr
reading sources... [ 91%] api
reading sources... [ 93%] benchmarks
reading sources... [ 94%] fileformat-prose
reading sources... [ 96%] index
reading sources... [ 98%] references
reading sources... [100%] release_notes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [  1%] anndata.AnnData
writing output... [  3%] anndata.AnnData.T
writing output... [  5%] anndata.AnnData.X
writing output... [  6%] anndata.AnnData.chunk_X
writing output... [  8%] anndata.AnnData.chunked_X
writing output... [ 10%] anndata.AnnData.concatenate
writing output... [ 12%] anndata.AnnData.copy
writing output... [ 13%] anndata.AnnData.filename
writing output... [ 15%] anndata.AnnData.is_view
writing output... [ 17%] anndata.AnnData.isbacked
writing output... [ 18%] anndata.AnnData.isview
writing output... [ 20%] anndata.AnnData.layers
writing output... [ 22%] anndata.AnnData.n_obs
writing output... [ 24%] anndata.AnnData.n_vars
writing output... [ 25%] anndata.AnnData.obs
writing output... [ 27%] anndata.AnnData.obs_keys
writing output... [ 29%] anndata.AnnData.obs_names
writing output... [ 31%] anndata.AnnData.obs_names_make_unique
writing output... [ 32%] anndata.AnnData.obs_vector
writing output... [ 34%] anndata.AnnData.obsm
writing output... [ 36%] anndata.AnnData.obsm_keys
writing output... [ 37%] anndata.AnnData.obsp
writing output... [ 39%] anndata.AnnData.raw
writing output... [ 41%] anndata.AnnData.rename_categories
writing output... [ 43%] anndata.AnnData.shape
writing output... [ 44%] anndata.AnnData.strings_to_categoricals
writing output... [ 46%] anndata.AnnData.to_df
writing output... [ 48%] anndata.AnnData.transpose
writing output... [ 50%] anndata.AnnData.uns
writing output... [ 51%] anndata.AnnData.uns_keys
writing output... [ 53%] anndata.AnnData.var
writing output... [ 55%] anndata.AnnData.var_keys
writing output... [ 56%] anndata.AnnData.var_names
writing output... [ 58%] anndata.AnnData.var_names_make_unique
writing output... [ 60%] anndata.AnnData.var_vector
writing output... [ 62%] anndata.AnnData.varm
writing output... [ 63%] anndata.AnnData.varm_keys
writing output... [ 65%] anndata.AnnData.varp
writing output... [ 67%] anndata.AnnData.write
writing output... [ 68%] anndata.AnnData.write_csvs
writing output... [ 70%] anndata.AnnData.write_h5ad
writing output... [ 72%] anndata.AnnData.write_loom
writing output... [ 74%] anndata.AnnData.write_zarr
writing output... [ 75%] anndata.read_csv
writing output... [ 77%] anndata.read_excel
writing output... [ 79%] anndata.read_h5ad
writing output... [ 81%] anndata.read_hdf
writing output... [ 82%] anndata.read_loom
writing output... [ 84%] anndata.read_mtx
writing output... [ 86%] anndata.read_text
writing output... [ 87%] anndata.read_umi_tools
writing output... [ 89%] anndata.read_zarr
writing output... [ 91%] api
writing output... [ 93%] benchmarks
writing output... [ 94%] fileformat-prose
writing output... [ 96%] index
writing output... [ 98%] references
writing output... [100%] release_notes

generating indices...  genindex py-modindexdone
writing additional pages...  searchdone
copying static files... ... done
copying readthedocs static files... done
copying searchtools... 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.
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable" is shallow and may cause errors
  warnings.warn('"{}" is shallow and may cause errors'.format(wd.path))
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx_rtd_theme/search.html:20: RemovedInSphinx30Warning: To modify script_files in the theme is deprecated. Please insert a <script> tag directly in your theme instead.
  {{ super() }}

[rtd-command-info] start-time: 2020-01-24T17:42:31.639242Z, end-time: 2020-01-24T17:42:44.394781Z, duration: 12, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v2.3.1
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...
[autosummary] generating autosummary for: api.rst, benchmarks.rst, fileformat-prose.rst, index.rst, references.rst, release_notes.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_csvs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_zarr.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_csv.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_excel.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_h5ad.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_hdf.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_loom.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_mtx.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_text.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_umi_tools.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.read_zarr.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.T.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunk_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.chunked_X.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.concatenate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.copy.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.filename.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.is_view.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isbacked.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.isview.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.uns_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_names_make_unique.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.var_vector.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varm_keys.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.varp.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/anndata.AnnData.write_h5ad.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: [new config] 58 added, 0 changed, 0 removed
reading sources... [  1%] anndata.AnnData
reading sources... [  3%] anndata.AnnData.T
reading sources... [  5%] anndata.AnnData.X
reading sources... [  6%] anndata.AnnData.chunk_X
reading sources... [  8%] 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
reading sources... [ 17%] anndata.AnnData.isbacked
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reading sources... [ 20%] anndata.AnnData.layers
reading sources... [ 22%] anndata.AnnData.n_obs
reading sources... [ 24%] anndata.AnnData.n_vars
reading sources... [ 25%] anndata.AnnData.obs
reading sources... [ 27%] anndata.AnnData.obs_keys
reading sources... [ 29%] anndata.AnnData.obs_names
reading sources... [ 31%] anndata.AnnData.obs_names_make_unique
reading sources... [ 32%] anndata.AnnData.obs_vector
reading sources... [ 34%] anndata.AnnData.obsm
reading sources... [ 36%] anndata.AnnData.obsm_keys
reading sources... [ 37%] anndata.AnnData.obsp
reading sources... [ 39%] anndata.AnnData.raw
reading sources... [ 41%] anndata.AnnData.rename_categories
reading sources... [ 43%] anndata.AnnData.shape
reading sources... [ 44%] anndata.AnnData.strings_to_categoricals
reading sources... [ 46%] anndata.AnnData.to_df
reading sources... [ 48%] anndata.AnnData.transpose
reading sources... [ 50%] anndata.AnnData.uns
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reading sources... [ 53%] anndata.AnnData.var
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reading sources... [ 67%] anndata.AnnData.write
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reading sources... [ 86%] anndata.read_text
reading sources... [ 87%] anndata.read_umi_tools
reading sources... [ 89%] anndata.read_zarr
reading sources... [ 91%] api
reading sources... [ 93%] benchmarks
reading sources... [ 94%] fileformat-prose
reading sources... [ 96%] index
reading sources... [ 98%] references
reading sources... [100%] release_notes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... api anndata.AnnData anndata.AnnData.T anndata.AnnData.X anndata.AnnData.filename anndata.AnnData.is_view anndata.AnnData.isbacked anndata.AnnData.isview anndata.AnnData.layers anndata.AnnData.n_obs anndata.AnnData.n_vars anndata.AnnData.obs anndata.AnnData.obs_names anndata.AnnData.obsm anndata.AnnData.obsp anndata.AnnData.raw anndata.AnnData.shape anndata.AnnData.uns anndata.AnnData.var anndata.AnnData.var_names anndata.AnnData.varm anndata.AnnData.varp anndata.AnnData.chunk_X anndata.AnnData.chunked_X anndata.AnnData.concatenate anndata.AnnData.copy anndata.AnnData.obs_keys anndata.AnnData.obs_names_make_unique anndata.AnnData.obs_vector anndata.AnnData.obsm_keys anndata.AnnData.rename_categories anndata.AnnData.strings_to_categoricals anndata.AnnData.to_df anndata.AnnData.transpose anndata.AnnData.uns_keys anndata.AnnData.var_keys anndata.AnnData.var_names_make_unique anndata.AnnData.var_vector anndata.AnnData.varm_keys anndata.AnnData.write anndata.AnnData.write_csvs anndata.AnnData.write_h5ad anndata.AnnData.write_loom anndata.AnnData.write_zarr anndata.read_h5ad anndata.read_csv anndata.read_excel anndata.read_hdf anndata.read_loom anndata.read_mtx anndata.read_text anndata.read_umi_tools anndata.read_zarr fileformat-prose benchmarks references done
writing... done
writing additional files... done
copying static files... ... done
copying readthedocs static files... done
copying extra files... done
dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.
/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable" is shallow and may cause errors
  warnings.warn('"{}" is shallow and may cause errors'.format(wd.path))