Read the Docs build information
Build id: 164018
Project: icb-anndata
Version: latest
Commit: 51be5d85e62b1aa19d6f55ffc21aedbe9628c4c5
Date: 2018-11-30T12:30:18.221084Z
State: finished
Success: True


[rtd-command-info] start-time: 2018-11-30T18:30:18.758854Z, end-time: 2018-11-30T18:30:19.369508Z, duration: 0, exit-code: 0
git clone https://github.com/theislab/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2018-11-30T18:30:19.440410Z, end-time: 2018-11-30T18:30:19.449792Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out 'origin/master'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at 51be5d8 output warnings for non-string indices

[rtd-command-info] start-time: 2018-11-30T18:30:19.510887Z, end-time: 2018-11-30T18:30:19.518354Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2018-11-30T18:30:19.603026Z, end-time: 2018-11-30T18:30:19.610615Z, duration: 0, exit-code: 0
git branch -r
origin/2d
  origin/HEAD -> origin/master
  origin/backed
  origin/master
  origin/strings_to_categories

[rtd-command-info] start-time: 2018-11-30T18:30:20.672373Z, end-time: 2018-11-30T18:30:23.419988Z, duration: 2, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.2'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python
Installing setuptools, pip, wheel...done.

[rtd-command-info] start-time: 2018-11-30T18:30:23.514760Z, end-time: 2018-11-30T18:30:49.421088Z, duration: 25, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
Collecting Pygments==2.2.0
  Downloading https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl (841kB)
Collecting setuptools<40
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Collecting docutils==0.13.1
  Downloading https://files.pythonhosted.org/packages/7c/30/8fb30d820c012a6f701a66618ce065b6d61d08ac0a77e47fc7808dbaee47/docutils-0.13.1-py3-none-any.whl (536kB)
Collecting mock==1.0.1
  Downloading https://files.pythonhosted.org/packages/a2/52/7edcd94f0afb721a2d559a5b9aae8af4f8f2c79bc63fdbe8a8a6c9b23bbe/mock-1.0.1.tar.gz (818kB)
Collecting pillow==2.6.1
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Collecting alabaster!=0.7.5,<0.8,>=0.7
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Collecting commonmark==0.5.4
  Downloading https://files.pythonhosted.org/packages/4d/93/3808cbcebe94d205f55a9a32857df733a603339d32c46cd32669d808d964/CommonMark-0.5.4.tar.gz (120kB)
Collecting recommonmark==0.4.0
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Collecting sphinx<1.8
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Collecting sphinx-rtd-theme<0.5
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Collecting Jinja2>=2.3 (from sphinx<1.8)
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Collecting snowballstemmer>=1.1 (from sphinx<1.8)
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Collecting six>=1.5 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting imagesize (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting packaging (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/89/d1/92e6df2e503a69df9faab187c684585f0136662c12bb1f36901d426f3fab/packaging-18.0-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/ff/17/5cbb026005115301a8fb2f9b0e3e8d32313142fe8b617070e7baad20554f/requests-2.20.1-py2.py3-none-any.whl (57kB)
Collecting babel!=2.0,>=1.3 (from sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl (8.1MB)
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/08/04/f2191b50fb7f0712f03f064b71d8b4605190f2178ba02e975a87f7b89a0d/MarkupSafe-1.1.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/71/e8/6777f6624681c8b9701a8a0a5654f3eb56919a01a78e12bf3c73f5a3c714/pyparsing-2.3.0-py2.py3-none-any.whl (59kB)
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl (133kB)
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/9f/e0/accfc1b56b57e9750eba272e24c4dddeac86852c2bebd1236674d7887e8a/certifi-2018.11.29-py2.py3-none-any.whl (154kB)
Collecting urllib3<1.25,>=1.21.1 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/62/00/ee1d7de624db8ba7090d1226aebefab96a2c71cd5cfa7629d6ad3f61b79e/urllib3-1.24.1-py2.py3-none-any.whl (118kB)
Collecting idna<2.8,>=2.5 (from requests>=2.0.0->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl (58kB)
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8)
  Downloading https://files.pythonhosted.org/packages/f8/0e/2365ddc010afb3d79147f1dd544e5ee24bf4ece58ab99b16fbb465ce6dc0/pytz-2018.7-py2.py3-none-any.whl (506kB)
Building wheels for collected packages: mock, pillow, commonmark
  Running setup.py bdist_wheel for mock: started
  Running setup.py bdist_wheel for mock: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/7e/72/92/744b532c779242b57aab4bcba80c312b30c069bbd60025e7e6
  Running setup.py bdist_wheel for pillow: started
  Running setup.py bdist_wheel for pillow: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/de/0e/6b/556798d1ac8762a076ddff5b20f65b2e6cc2ae13b0e683c263
  Running setup.py bdist_wheel for commonmark: started
  Running setup.py bdist_wheel for commonmark: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip/wheels/a0/f4/35/019d917f6875107ade3aad634c982f5c6b604c5631cddf20ac
Successfully built mock pillow commonmark
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, MarkupSafe, Jinja2, snowballstemmer, sphinxcontrib-websupport, six, imagesize, pyparsing, packaging, chardet, certifi, urllib3, idna, requests, pytz, babel, sphinx, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 39.0.1
    Uninstalling setuptools-39.0.1:
      Successfully uninstalled setuptools-39.0.1
Successfully installed Jinja2-2.10 MarkupSafe-1.1.0 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 certifi-2018.11.29 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.7 imagesize-1.1.0 mock-1.0.1 packaging-18.0 pillow-2.6.1 pyparsing-2.3.0 pytz-2018.7 readthedocs-sphinx-ext-0.5.15 recommonmark-0.4.0 requests-2.20.1 setuptools-39.2.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.2 sphinxcontrib-websupport-1.1.0 urllib3-1.24.1
You are using pip version 9.0.3, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-11-30T18:30:49.487823Z, end-time: 2018-11-30T18:31:08.397234Z, duration: 18, exit-code: 0
python 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~=1.7.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 2))
Collecting sphinx-autodoc-typehints (from -r docs/requires.txt (line 3))
  Downloading https://files.pythonhosted.org/packages/37/8e/0bd53face2d3c1ac556467f171bf9595604b2cce06bae3bc72722014064f/sphinx_autodoc_typehints-1.5.1-py3-none-any.whl
Collecting pandas~=0.21 (from -r docs/requires.txt (line 5))
  Downloading https://files.pythonhosted.org/packages/e1/d8/feeb346d41f181e83fba45224ab14a8d8af019b48af742e047f3845d8cff/pandas-0.23.4-cp36-cp36m-manylinux1_x86_64.whl (8.9MB)
Collecting scipy (from -r docs/requires.txt (line 6))
  Downloading https://files.pythonhosted.org/packages/a8/0b/f163da98d3a01b3e0ef1cab8dd2123c34aee2bafbb1c5bffa354cc8a1730/scipy-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (31.2MB)
Collecting h5py (from -r docs/requires.txt (line 7))
  Downloading https://files.pythonhosted.org/packages/8e/cb/726134109e7bd71d98d1fcc717ffe051767aac42ede0e7326fd1787e5d64/h5py-2.8.0-cp36-cp36m-manylinux1_x86_64.whl (2.8MB)
Collecting natsort (from -r docs/requires.txt (line 8))
  Downloading https://files.pythonhosted.org/packages/d8/67/9f795649f1173b18851941e288035695386ee44c33bb0960832550f8a236/natsort-5.5.0-py2.py3-none-any.whl
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~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx~=1.7.3->-r docs/requires.txt (line 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~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
Collecting numpy>=1.9.0 (from pandas~=0.21->-r docs/requires.txt (line 5))
  Downloading https://files.pythonhosted.org/packages/ff/7f/9d804d2348471c67a7d8b5f84f9bc59fd1cefa148986f2b74552f8573555/numpy-1.15.4-cp36-cp36m-manylinux1_x86_64.whl (13.9MB)
Collecting python-dateutil>=2.5.0 (from pandas~=0.21->-r docs/requires.txt (line 5))
  Downloading https://files.pythonhosted.org/packages/74/68/d87d9b36af36f44254a8d512cbfc48369103a3b9e474be9bdfe536abfc45/python_dateutil-2.7.5-py2.py3-none-any.whl (225kB)
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 5))
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~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: idna<2.8,>=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~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: 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~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: urllib3<1.25,>=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~=1.7.3->-r docs/requires.txt (line 2))
Requirement already satisfied: 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~=1.7.3->-r docs/requires.txt (line 2))
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~=1.7.3->-r docs/requires.txt (line 2))
Installing collected packages: sphinx-autodoc-typehints, numpy, python-dateutil, pandas, scipy, h5py, natsort
Successfully installed h5py-2.8.0 natsort-5.5.0 numpy-1.15.4 pandas-0.23.4 python-dateutil-2.7.5 scipy-1.1.0 sphinx-autodoc-typehints-1.5.1
You are using pip version 9.0.3, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-11-30T18:31:08.905400Z, end-time: 2018-11-30T18:31:08.972226Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import time
import inspect
from pathlib import Path, PurePosixPath
import logging

HERE = Path(__file__).parent
sys.path.insert(0, str(HERE / '..'))

import anndata


logger = logging.getLogger(__name__)

for generated in HERE.glob('anndata.*.rst'):
    generated.unlink()


# -- General configuration ------------------------------------------------

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
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',
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_mock_imports = ['_tkinter']  # why this?
autodoc_member_order = 'bysource'
#autodoc_default_flags = ['members']
napoleon_use_rtype = False
napoleon_use_param = True

intersphinx_mapping = dict(
    python=('https://docs.python.org/3', None),
    h5py=('http://docs.h5py.org/en/latest/', None)
)

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
project = 'anndata'
copyright = '{}, Alex Wolf, Philipp Angerer, Sergei Rybakov'.format(time.strftime("%Y"))
author = 'Alex Wolf, Philipp Angerer, Sergei Rybakov'

version = anndata.__version__.replace('.dirty', '')
release = version
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'
todo_include_todos = False

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

html_theme = 'sphinx_rtd_theme'
html_theme_options = {
    'navigation_depth': 2,
}
html_context = {
    '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
    'css_files': [               # Additional CSS
        '_static/css/override.css',
    ],
}
if 'READTHEDOCS' in os.environ:
    # For some reason, RTD doesn’t insert their stuff anymore once we add custom CSS files.
    html_context['css_files'].insert(0, 'https://media.readthedocs.org/css/sphinx_rtd_theme.css')

html_static_path = ['_static']

# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'anndatadoc'


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'anndata.tex', 'anndata Documentation',
     'Alex Wolf, Philipp Angerer', 'manual'),
]


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'anndata', 'anndata Documentation',
     [author], 1)
]


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'anndata', 'anndata Documentation',
     author, 'anndata', 'One line description of project.',
     'Miscellaneous'),
]


# -- GitHub links ---------------------------------------------------------


def get_obj_module(qualname):
    """Get a module/class/attribute and its original module by qualname"""
    modname = qualname
    classname = None
    attrname = None
    while modname not in sys.modules:
        attrname = classname
        modname, classname = modname.rsplit('.', 1)

    # retrieve object and find original module name
    if classname:
        cls = getattr(sys.modules[modname], classname)
        modname = cls.__module__
        obj = getattr(cls, attrname) if attrname else cls
    else:
        obj = None

    return obj, sys.modules[modname]


def get_linenos(obj):
    """Get an object’s line numbers"""
    try:
        lines, start = inspect.getsourcelines(obj)
    except TypeError:
        return None, None
    else:
        return start, start + len(lines) - 1


project_dir = Path(__file__).parent.parent  # project/docs/conf.py/../.. → project/
github_url1 = 'https://github.com/{github_user}/{github_repo}/tree/{github_version}'.format_map(html_context)
github_url2 = 'https://github.com/theislab/anndata/tree/master'


def modurl(qualname):
    """Get the full GitHub URL for some object’s qualname."""
    obj, module = get_obj_module(qualname)
    github_url = github_url1
    try:
        path = PurePosixPath(Path(module.__file__).resolve().relative_to(project_dir))
    except ValueError:
        # trying to document something from another package
        github_url = github_url2
        path = '/'.join(module.__file__.split('/')[-2:])
    start, end = get_linenos(obj)
    fragment = '#L{}-L{}'.format(start, end) if start and end else ''
    return '{}/{}{}'.format(github_url, path, fragment)


# html_context doesn’t apply to autosummary templates ☹
# and there’s no way to insert filters into those templates
# so we have to modify the default filters
from jinja2.defaults import DEFAULT_FILTERS

DEFAULT_FILTERS['modurl'] = modurl


# -- Prettier Param docs --------------------------------------------


from typing import Dict, List, Tuple

from docutils import nodes
from sphinx import addnodes
from sphinx.domains.python import PyTypedField, PyObject
from sphinx.environment import BuildEnvironment


class PrettyTypedField(PyTypedField):
    list_type = nodes.definition_list
    
    def make_field(
        self,
        types: Dict[str, List[nodes.Node]],
        domain: str,
        items: Tuple[str, List[nodes.inline]],
        env: BuildEnvironment = None
    ) -> nodes.field:
        def makerefs(rolename, name, node):
            return self.make_xrefs(rolename, domain, name, node, env=env)
        
        def handle_item(fieldarg: str, content: List[nodes.inline]) -> nodes.definition_list_item:
            head = nodes.term()
            head += makerefs(self.rolename, fieldarg, addnodes.literal_strong)
            fieldtype = types.pop(fieldarg, None)
            if fieldtype is not None:
                head += nodes.Text(' : ')
                if len(fieldtype) == 1 and isinstance(fieldtype[0], nodes.Text):
                    typename = ''.join(n.astext() for n in fieldtype)
                    head += makerefs(self.typerolename, typename, addnodes.literal_emphasis)
                else:
                    head += fieldtype

            body_content = nodes.paragraph('', '', *content)
            body = nodes.definition('', body_content)

            return nodes.definition_list_item('', head, body)

        fieldname = nodes.field_name('', self.label)
        if len(items) == 1 and self.can_collapse:
            fieldarg, content = items[0]
            bodynode = handle_item(fieldarg, content)
        else:
            bodynode = self.list_type()
            for fieldarg, content in items:
                bodynode += handle_item(fieldarg, content)
        fieldbody = nodes.field_body('', bodynode)
        return nodes.field('', fieldname, fieldbody)


# replace matching field types with ours
PyObject.doc_field_types = [
    PrettyTypedField(
        ft.name,
        names=ft.names,
        typenames=ft.typenames,
        label=ft.label,
        rolename=ft.rolename,
        typerolename=ft.typerolename,
        can_collapse=ft.can_collapse,
    ) if isinstance(ft, PyTypedField) else ft
    for ft in PyObject.doc_field_types
]





###########################################################################
#          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
    else:
        SUFFIX = source_suffix[0]
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')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_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': [ 
    ("htmlzip", "//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/latest/',
    'analytics_code': '',
    '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': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '51be5d85',
}




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"]

[rtd-command-info] start-time: 2018-11-30T18:31:09.034986Z, end-time: 2018-11-30T18:31:16.193027Z, duration: 7, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from http://docs.h5py.org/en/latest/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.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_keys.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.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.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.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.Dataset.fletcher32.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
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 5 source files that are out of date
updating environment: 96 added, 0 changed, 0 removed
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generating indices... genindex py-modindex
writing additional pages... search
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dumping search index in English (code: en) ... done
dumping object inventory... done
build succeeded, 4 warnings.

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2018-11-30T18:31:16.323737Z, end-time: 2018-11-30T18:31:21.521812Z, duration: 5, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading pickled environment... not yet created
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from http://docs.h5py.org/en/latest/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.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/anndata.AnnData.var_keys.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.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.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.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.Dataset.fletcher32.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
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 96 added, 0 changed, 0 removed
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dumping object inventory... done
build succeeded, 4 warnings.

The HTML page is in _build/localmedia.