Read the Docs build information
Build id: 272062
Project: icb-scanpy-tutorials
Version: latest
Commit: ceafdf3d7a126111dfd6cd151c2a5abd2d183096
Date: 2019-12-25T16:36:41.632005Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-12-25T16:36:42.089689Z, end-time: 2019-12-25T16:36:46.929906Z, duration: 4, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-12-25T16:36:47.148704Z, end-time: 2019-12-25T16:36:47.268987Z, 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 ceafdf3 migrated clustering tutorial to leiden algo and normalize_total for 1.4.5

[rtd-command-info] start-time: 2019-12-25T16:36:47.346245Z, end-time: 2019-12-25T16:36:47.355726Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-12-25T16:36:48.221862Z, end-time: 2019-12-25T16:36:52.669303Z, 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-scanpy-tutorials/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-12-25T16:36:52.767113Z, end-time: 2019-12-25T16:36:55.196128Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip pip
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Installing collected packages: pip
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    Uninstalling pip-19.1.1:
      Successfully uninstalled pip-19.1.1
Successfully installed pip-19.3.1

[rtd-command-info] start-time: 2019-12-25T16:36:55.352431Z, end-time: 2019-12-25T16:37:06.206906Z, duration: 10, exit-code: 0
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[rtd-command-info] start-time: 2019-12-25T16:37:06.302192Z, end-time: 2019-12-25T16:37:35.388767Z, duration: 29, exit-code: 0
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  Downloading https://files.pythonhosted.org/packages/9a/41/220f49aaea88bc6fa6cba8d05ecf24676326156c23b991e80b3f2fc24c77/pickleshare-0.7.5-py2.py3-none-any.whl
Collecting pexpect; sys_platform != "win32"
  Downloading https://files.pythonhosted.org/packages/0e/3e/377007e3f36ec42f1b84ec322ee12141a9e10d808312e5738f52f80a232c/pexpect-4.7.0-py2.py3-none-any.whl (58kB)
Collecting backcall
  Downloading https://files.pythonhosted.org/packages/84/71/c8ca4f5bb1e08401b916c68003acf0a0655df935d74d93bf3f3364b310e0/backcall-0.1.0.tar.gz
Collecting ipython-genutils
  Downloading https://files.pythonhosted.org/packages/fa/bc/9bd3b5c2b4774d5f33b2d544f1460be9df7df2fe42f352135381c347c69a/ipython_genutils-0.2.0-py2.py3-none-any.whl
Collecting jsonschema!=2.5.0,>=2.4
  Downloading https://files.pythonhosted.org/packages/c5/8f/51e89ce52a085483359217bc72cdbf6e75ee595d5b1d4b5ade40c7e018b8/jsonschema-3.2.0-py2.py3-none-any.whl (56kB)
Collecting bleach
  Downloading https://files.pythonhosted.org/packages/ab/05/27e1466475e816d3001efb6e0a85a819be17411420494a1e602c36f8299d/bleach-3.1.0-py2.py3-none-any.whl (157kB)
Collecting mistune<2,>=0.8.1
  Downloading https://files.pythonhosted.org/packages/09/ec/4b43dae793655b7d8a25f76119624350b4d65eb663459eb9603d7f1f0345/mistune-0.8.4-py2.py3-none-any.whl
Collecting testpath
  Downloading https://files.pythonhosted.org/packages/1b/9e/1a170feaa54f22aeb5a5d16c9015e82234275a3c8ab630b552493f9cb8a9/testpath-0.4.4-py2.py3-none-any.whl (163kB)
Collecting defusedxml
  Downloading https://files.pythonhosted.org/packages/06/74/9b387472866358ebc08732de3da6dc48e44b0aacd2ddaa5cb85ab7e986a2/defusedxml-0.6.0-py2.py3-none-any.whl
Collecting entrypoints>=0.2.2
  Downloading https://files.pythonhosted.org/packages/ac/c6/44694103f8c221443ee6b0041f69e2740d89a25641e62fb4f2ee568f2f9c/entrypoints-0.3-py2.py3-none-any.whl
Collecting pandocfilters>=1.4.1
  Downloading https://files.pythonhosted.org/packages/4c/ea/236e2584af67bb6df960832731a6e5325fd4441de001767da328c33368ce/pandocfilters-1.4.2.tar.gz
Collecting kiwisolver>=1.0.1
  Downloading https://files.pythonhosted.org/packages/f8/a1/5742b56282449b1c0968197f63eae486eca2c35dcd334bab75ad524e0de1/kiwisolver-1.1.0-cp36-cp36m-manylinux1_x86_64.whl (90kB)
Collecting cycler>=0.10
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Collecting sqlalchemy
  Downloading https://files.pythonhosted.org/packages/17/7f/35879c73859368ad19a952b69ee780aa97fc30350dabd45fb948d6a4e3ea/SQLAlchemy-1.3.12.tar.gz (6.0MB)
Collecting jupyter
  Downloading https://files.pythonhosted.org/packages/83/df/0f5dd132200728a86190397e1ea87cd76244e42d39ec5e88efd25b2abd7e/jupyter-1.0.0-py2.py3-none-any.whl
Collecting notebook>=4.2
  Downloading https://files.pythonhosted.org/packages/f5/69/d2ffaf7efc20ce47469187e3a41e6e03e17b45de5a6559f4e7ab3eace5e1/notebook-6.0.2-py3-none-any.whl (9.7MB)
Collecting alembic
  Downloading https://files.pythonhosted.org/packages/dc/6d/3c1411dfdcf089ec89ce5e2222deb2292f39b6b1a5911222e15af9fe5a92/alembic-1.3.2.tar.gz (1.1MB)
Collecting fuzzywuzzy
  Downloading https://files.pythonhosted.org/packages/d8/f1/5a267addb30ab7eaa1beab2b9323073815da4551076554ecc890a3595ec9/fuzzywuzzy-0.17.0-py2.py3-none-any.whl
Collecting parso>=0.5.2
  Downloading https://files.pythonhosted.org/packages/9b/b0/90353a5ece0987279837835224dead0c424833a224195683e188d384e06b/parso-0.5.2-py2.py3-none-any.whl (99kB)
Collecting wcwidth
  Downloading https://files.pythonhosted.org/packages/7e/9f/526a6947247599b084ee5232e4f9190a38f398d7300d866af3ab571a5bfe/wcwidth-0.1.7-py2.py3-none-any.whl
Collecting ptyprocess>=0.5
  Downloading https://files.pythonhosted.org/packages/d1/29/605c2cc68a9992d18dada28206eeada56ea4bd07a239669da41674648b6f/ptyprocess-0.6.0-py2.py3-none-any.whl
Collecting attrs>=17.4.0
  Downloading https://files.pythonhosted.org/packages/a2/db/4313ab3be961f7a763066401fb77f7748373b6094076ae2bda2806988af6/attrs-19.3.0-py2.py3-none-any.whl
Collecting importlib-metadata; python_version < "3.8"
  Downloading https://files.pythonhosted.org/packages/e9/71/1a1e0ed0981bb6a67bce55a210f168126b7ebd2065958673797ea66489ca/importlib_metadata-1.3.0-py2.py3-none-any.whl
Collecting pyrsistent>=0.14.0
  Downloading https://files.pythonhosted.org/packages/6c/6f/c1a2e8da80a0029f6b618d7e20e1a6f2a61dd04e2e54225309c2cc4268f7/pyrsistent-0.15.6.tar.gz (107kB)
Collecting webencodings
  Downloading https://files.pythonhosted.org/packages/f4/24/2a3e3df732393fed8b3ebf2ec078f05546de641fe1b667ee316ec1dcf3b7/webencodings-0.5.1-py2.py3-none-any.whl
Collecting jupyter-console
  Downloading https://files.pythonhosted.org/packages/cb/ee/6374ae8c21b7d0847f9c3722dcdfac986b8e54fa9ad9ea66e1eb6320d2b8/jupyter_console-6.0.0-py2.py3-none-any.whl
Collecting ipywidgets
  Downloading https://files.pythonhosted.org/packages/56/a0/dbcf5881bb2f51e8db678211907f16ea0a182b232c591a6d6f276985ca95/ipywidgets-7.5.1-py2.py3-none-any.whl (121kB)
Collecting qtconsole
  Downloading https://files.pythonhosted.org/packages/7c/57/3528b84ffa753e2089908bbf74bb5ae60653eb7a63797b6234e88b847d67/qtconsole-4.6.0-py2.py3-none-any.whl (121kB)
Collecting Send2Trash
  Downloading https://files.pythonhosted.org/packages/49/46/c3dc27481d1cc57b9385aff41c474ceb7714f7935b1247194adae45db714/Send2Trash-1.5.0-py3-none-any.whl
Collecting prometheus-client
  Downloading https://files.pythonhosted.org/packages/b3/23/41a5a24b502d35a4ad50a5bb7202a5e1d9a0364d0c12f56db3dbf7aca76d/prometheus_client-0.7.1.tar.gz
Collecting terminado>=0.8.1
  Downloading https://files.pythonhosted.org/packages/ff/96/1d9a2c23990aea8f8e0b5c3b6627d03196a73771a17a2d9860bbe9823ab6/terminado-0.8.3-py2.py3-none-any.whl
Collecting Mako
  Downloading https://files.pythonhosted.org/packages/b0/3c/8dcd6883d009f7cae0f3157fb53e9afb05a0d3d33b3db1268ec2e6f4a56b/Mako-1.1.0.tar.gz (463kB)
Collecting python-editor>=0.3
  Downloading https://files.pythonhosted.org/packages/c6/d3/201fc3abe391bbae6606e6f1d598c15d367033332bd54352b12f35513717/python_editor-1.0.4-py3-none-any.whl
Collecting zipp>=0.5
  Downloading https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Collecting widgetsnbextension~=3.5.0
  Downloading https://files.pythonhosted.org/packages/6c/7b/7ac231c20d2d33c445eaacf8a433f4e22c60677eb9776c7c5262d7ddee2d/widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2MB)
Collecting more-itertools
  Downloading https://files.pythonhosted.org/packages/68/03/0604cec1ea13c9f063dd50f900d1a36160334dd3cfb01fd0e638f61b46ba/more_itertools-8.0.2-py3-none-any.whl (40kB)
Building wheels for collected packages: tornado, nbgrader, backcall, pandocfilters, sqlalchemy, alembic, pyrsistent, prometheus-client, Mako
  Building wheel for tornado (setup.py): started
  Building wheel for tornado (setup.py): finished with status 'done'
  Created wheel for tornado: filename=tornado-6.0.3-cp36-cp36m-linux_x86_64.whl size=423199 sha256=d91981e5ea752bad5c2e84becdb7c25af4bf1f99174d60f1019d6616a83a738b
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/84/bf/40/2f6ef700f48401ca40e5e3dd7d0e3c0a90e064897b7fe5fc08
  Building wheel for nbgrader (setup.py): started
  Building wheel for nbgrader (setup.py): finished with status 'done'
  Created wheel for nbgrader: filename=nbgrader-0.6.1-cp36-none-any.whl size=13507857 sha256=6808b348fb7279b4eb100a7a09a7a7ee96c317ee8d76e02d41f582d3f38bbb2a
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/22/00/61/991b052f161819b207471e4d9b22418010530681be8b6dc35c
  Building wheel for backcall (setup.py): started
  Building wheel for backcall (setup.py): finished with status 'done'
  Created wheel for backcall: filename=backcall-0.1.0-cp36-none-any.whl size=10414 sha256=37ca78fc8d0e54f4db13387bc154da148c2888af56a8a01eeb64f4e2d7fde5ab
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/b0/dd/29e28ff615af3dda4c67cab719dd51357597eabff926976b45
  Building wheel for pandocfilters (setup.py): started
  Building wheel for pandocfilters (setup.py): finished with status 'done'
  Created wheel for pandocfilters: filename=pandocfilters-1.4.2-cp36-none-any.whl size=7857 sha256=752f506cb6314dae38d0267e324fde0318d580f3a8a881778d8a96d4c8fe6a85
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/39/01/56/f1b08a6275acc59e846fa4c1e1b65dbc1919f20157d9e66c20
  Building wheel for sqlalchemy (setup.py): started
  Building wheel for sqlalchemy (setup.py): finished with status 'done'
  Created wheel for sqlalchemy: filename=SQLAlchemy-1.3.12-cp36-cp36m-linux_x86_64.whl size=1215373 sha256=60e438c55703f4a9a3e470dee4dbb057e4feb306fba152f89148f3cca3c20ecb
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/ee/33/44/0788a6e806866ae2e246d5cd841d07498a46bcb3f3c42ea5a4
  Building wheel for alembic (setup.py): started
  Building wheel for alembic (setup.py): finished with status 'done'
  Created wheel for alembic: filename=alembic-1.3.2-py2.py3-none-any.whl size=151127 sha256=eb45211e96ecc1c6bce5521833f14da4629d1c3cb3b47430e8d2334f20df329b
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/5c/66/53/e0633382ac8625ab1c099db6a290d1b6b24f849a4666a57105
  Building wheel for pyrsistent (setup.py): started
  Building wheel for pyrsistent (setup.py): finished with status 'done'
  Created wheel for pyrsistent: filename=pyrsistent-0.15.6-cp36-cp36m-linux_x86_64.whl size=114945 sha256=9fe91838d429383d6bfb606ba703b711e22559cdca4f254e23cbb0a755214191
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/83/89/d3/1712b9c33c9b9c0911b188a86aeff2a9a05e113f986cf79d92
  Building wheel for prometheus-client (setup.py): started
  Building wheel for prometheus-client (setup.py): finished with status 'done'
  Created wheel for prometheus-client: filename=prometheus_client-0.7.1-cp36-none-any.whl size=41406 sha256=4740e478d9dcea3956c30e967cbb3a09b22bd07e1555848ce93cfbf37334341b
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/1c/54/34/fd47cd9b308826cc4292b54449c1899a30251ef3b506bc91ea
  Building wheel for Mako (setup.py): started
  Building wheel for Mako (setup.py): finished with status 'done'
  Created wheel for Mako: filename=Mako-1.1.0-cp36-none-any.whl size=75361 sha256=1756666b2d2ee08a4796c4d6c01e3ac16eccb25728acc74fb5fe431230b102d6
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/98/32/7b/a291926643fc1d1e02593e0d9e247c5a866a366b8343b7aa27
Successfully built tornado nbgrader backcall pandocfilters sqlalchemy alembic pyrsistent prometheus-client Mako
ERROR: jupyter-console 6.0.0 has requirement prompt-toolkit<2.1.0,>=2.0.0, but you'll have prompt-toolkit 3.0.2 which is incompatible.
Installing collected packages: tornado, decorator, ipython-genutils, traitlets, jupyter-core, pyzmq, python-dateutil, jupyter-client, parso, jedi, wcwidth, prompt-toolkit, pickleshare, ptyprocess, pexpect, backcall, ipython, ipykernel, attrs, more-itertools, zipp, importlib-metadata, pyrsistent, jsonschema, nbformat, webencodings, bleach, mistune, testpath, defusedxml, entrypoints, pandocfilters, nbconvert, nbsphinx, numpy, kiwisolver, cycler, matplotlib, tqdm, sqlalchemy, jupyter-console, Send2Trash, prometheus-client, terminado, notebook, widgetsnbextension, ipywidgets, qtconsole, jupyter, Mako, python-editor, alembic, fuzzywuzzy, nbgrader, nbclean
Successfully installed Mako-1.1.0 Send2Trash-1.5.0 alembic-1.3.2 attrs-19.3.0 backcall-0.1.0 bleach-3.1.0 cycler-0.10.0 decorator-4.4.1 defusedxml-0.6.0 entrypoints-0.3 fuzzywuzzy-0.17.0 importlib-metadata-1.3.0 ipykernel-5.1.3 ipython-7.10.2 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.15.2 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-5.3.4 jupyter-console-6.0.0 jupyter-core-4.6.1 kiwisolver-1.1.0 matplotlib-3.1.2 mistune-0.8.4 more-itertools-8.0.2 nbclean-0.3.2 nbconvert-5.6.1 nbformat-4.4.0 nbgrader-0.6.1 nbsphinx-0.5.0 notebook-6.0.2 numpy-1.18.0 pandocfilters-1.4.2 parso-0.5.2 pexpect-4.7.0 pickleshare-0.7.5 prometheus-client-0.7.1 prompt-toolkit-3.0.2 ptyprocess-0.6.0 pyrsistent-0.15.6 python-dateutil-2.8.1 python-editor-1.0.4 pyzmq-18.1.1 qtconsole-4.6.0 sqlalchemy-1.3.12 terminado-0.8.3 testpath-0.4.4 tornado-6.0.3 tqdm-4.41.0 traitlets-4.3.3 wcwidth-0.1.7 webencodings-0.5.1 widgetsnbextension-3.5.1 zipp-0.6.0

[rtd-command-info] start-time: 2019-12-25T16:37:35.973402Z, end-time: 2019-12-25T16:37:36.191463Z, duration: 0, exit-code: 0
cat conf.py
from datetime import datetime
project = 'Scanpy'
author = 'Alex Wolf, Fidel Ramirez, Sergei Rybakov'
copyright = f'{datetime.now():%Y}, {author}.'

version = ''
release = version

extensions = [
    'nbsphinx',
]

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
language = None
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
pygments_style = 'sphinx'

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

html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=2, logo_only=True  # Only show the logo
)
html_context = dict(
    display_github=True,      # Integrate GitHub
    github_user='theislab',   # Username
    github_repo='scanpy-tutorials',     # Repo name
    github_version='master',  # Version
    conf_py_path='/',    # Path in the checkout to the docs root
)
html_static_path = ['_static']
html_show_sphinx = False
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'

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

# -- Strip output ----------------------------------------------

import nbclean, glob

for filename in glob.glob('**/*.ipynb', recursive=True):
    ntbk = nbclean.NotebookCleaner(filename)
    ntbk.clear('stderr')
    ntbk.save(filename)




###########################################################################
#          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': "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/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-scanpy-tutorials/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy-tutorials',
    'name': u'scanpy-tutorials',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-scanpy-tutorials.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'proxied_api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    'github_repo': 'scanpy-tutorials',
    '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': 'ceafdf3d',
}




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: 2019-12-25T16:37:36.274129Z, end-time: 2019-12-25T16:37:45.235069Z, duration: 8, 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...
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: 6 added, 0 changed, 0 removed
reading sources... [ 16%] README
reading sources... [ 33%] index
reading sources... [ 50%] integrating-pbmcs-using-ingest
reading sources... [ 66%] paga-paul15
reading sources... [ 83%] pbmc3k
reading sources... [100%] visualizing-marker-genes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [ 16%] README
writing output... [ 33%] index
writing output... [ 50%] integrating-pbmcs-using-ingest
writing output... [ 66%] paga-paul15
writing output... [ 83%] pbmc3k
writing output... [100%] visualizing-marker-genes

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

The HTML pages are in _build/html.

[rtd-command-info] start-time: 2019-12-25T16:37:45.408712Z, end-time: 2019-12-25T16:37:53.978814Z, duration: 8, 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...
building [mo]: targets for 0 po files that are out of date
building [readthedocssinglehtmllocalmedia]: all documents
updating environment: 6 added, 0 changed, 0 removed
reading sources... [ 16%] README
reading sources... [ 33%] index
reading sources... [ 50%] integrating-pbmcs-using-ingest
reading sources... [ 66%] paga-paul15
reading sources... [ 83%] pbmc3k
reading sources... [100%] visualizing-marker-genes

looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
assembling single document... pbmc3k paga-paul15 visualizing-marker-genes integrating-pbmcs-using-ingest 
writing... done
writing additional files...
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copying static files... done
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dumping object inventory... done
build succeeded.

The HTML page is in _build/localmedia.