Read the Docs build information
Build id: 176006
Project: icb-scanpy-tutorials
Version: latest
Commit: b5342f081747167e7d8d37515ab742bdc5187913
Date: 2019-01-21T12:47:15.967505Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-01-21T12:47:17.340665Z, end-time: 2019-01-21T12:47:19.424594Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-01-21T12:47:19.631147Z, end-time: 2019-01-21T12:47:19.710943Z, 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 b5342f0 added note sections in pbmc3k

[rtd-command-info] start-time: 2019-01-21T12:47:19.798153Z, end-time: 2019-01-21T12:47:19.804599Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-01-21T12:47:20.626328Z, end-time: 2019-01-21T12:47:22.704810Z, duration: 2, exit-code: 0
python2.7 -mvirtualenv --no-site-packages --no-download 
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/bin/python2.7
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: 2019-01-21T12:47:22.770038Z, end-time: 2019-01-21T12:47:24.740317Z, duration: 1, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip pip
Collecting pip
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Installing collected packages: pip
  Found existing installation: pip 9.0.1
    Uninstalling pip-9.0.1:
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Successfully installed pip-18.1

[rtd-command-info] start-time: 2019-01-21T12:47:24.799767Z, end-time: 2019-01-21T12:47:44.030907Z, duration: 19, exit-code: 0
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Successfully built mock pillow commonmark
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    Uninstalling setuptools-28.8.0:
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[rtd-command-info] start-time: 2019-01-21T12:47:44.095216Z, end-time: 2019-01-21T12:47:52.909055Z, duration: 8, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip -r /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/requirements.txt
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Collecting entrypoints>=0.2.2 (from nbconvert!=5.4->nbsphinx==0.3.5->-r /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/requirements.txt (line 3))
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Collecting jsonschema!=2.5.0,>=2.4 (from nbformat->nbsphinx==0.3.5->-r /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/requirements.txt (line 3))
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Building wheels for collected packages: tornado, simplegeneric, pandocfilters, scandir, configparser, functools32
  Running setup.py bdist_wheel for tornado: started
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  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/.cache/pip/wheels/6d/e1/ce/f4ee2fa420cc6b940123c64992b81047816d0a9fad6b879325
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Successfully built tornado simplegeneric pandocfilters scandir configparser functools32
Installing collected packages: scandir, pathlib2, pickleshare, simplegeneric, enum34, decorator, ipython-genutils, traitlets, backports.shutil-get-terminal-size, ptyprocess, pexpect, wcwidth, prompt-toolkit, ipython, futures, singledispatch, backports-abc, tornado, python-dateutil, pyzmq, jupyter-core, jupyter-client, ipykernel, webencodings, bleach, functools32, jsonschema, nbformat, mistune, testpath, configparser, entrypoints, pandocfilters, nbconvert, nbsphinx
Successfully installed backports-abc-0.5 backports.shutil-get-terminal-size-1.0.0 bleach-3.1.0 configparser-3.5.0 decorator-4.3.0 entrypoints-0.3 enum34-1.1.6 functools32-3.2.3.post2 futures-3.2.0 ipykernel-4.10.0 ipython-5.8.0 ipython-genutils-0.2.0 jsonschema-2.6.0 jupyter-client-5.2.4 jupyter-core-4.4.0 mistune-0.8.4 nbconvert-5.3.1 nbformat-4.4.0 nbsphinx-0.3.5 pandocfilters-1.4.2 pathlib2-2.3.3 pexpect-4.6.0 pickleshare-0.7.5 prompt-toolkit-1.0.15 ptyprocess-0.6.0 python-dateutil-2.7.5 pyzmq-17.1.2 scandir-1.9.0 simplegeneric-0.8.1 singledispatch-3.4.0.3 testpath-0.4.2 tornado-5.1.1 traitlets-4.3.2 wcwidth-0.1.7 webencodings-0.5.1

[rtd-command-info] start-time: 2019-01-21T12:47:53.390647Z, end-time: 2019-01-21T12:47:53.452271Z, duration: 0, exit-code: 0
cat conf.py
project = 'Scanpy'
copyright = '2018, Scanpy authors'
author = 'Scanpy authors'

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,
)
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']

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





###########################################################################
#          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')

# 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': [ 
    ],
    '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',
    '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': 'b5342f08',
}




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: 2019-01-21T12:47:53.515457Z, end-time: 2019-01-21T12:47:58.749425Z, duration: 5, exit-code: 0
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
loading translations [en]... done
making output directory...
loading pickled environment... not yet created
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[rtd-command-info] start-time: 2019-01-21T12:47:58.860279Z, end-time: 2019-01-21T12:48:03.600110Z, duration: 4, exit-code: 0
python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia
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[rtd-command-info] start-time: 2019-01-21T12:48:03.721040Z, end-time: 2019-01-21T12:48:08.149738Z, duration: 4, exit-code: 0
python sphinx-build -b latex -D language=en -d _build/doctrees . _build/latex
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[rtd-command-info] start-time: 2019-01-21T12:48:08.212610Z, end-time: 2019-01-21T12:48:21.663606Z, duration: 13, exit-code: 0
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Chapter 1.
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Chapter 2.
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[rtd-command-info] start-time: 2019-01-21T12:48:21.726149Z, end-time: 2019-01-21T12:48:21.850456Z, duration: 0, exit-code: 0
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Chapter 1.
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Chapter 2.
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Underfull \hbox (badness 5374) in paragraph at lines 1242--1244
\T1/ptm/m/n/10 For con-ve-nience, all of the pre-vi-ous func-tions are di-rectl
y avail-able for vi-su-al-iz-ing re-sults of \T1/pcr/m/n/10 tl.
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<use visualizing-marker-genes_64_0.png> (./Scanpy.ind) [39 <./visualizing-marke
r-genes_62_0.png>] [40 <./visualizing-marker-genes_64_0.png>] (./Scanpy.aux) )
(see the transcript file for additional information){/usr/share/texlive/texmf-d
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Output written on Scanpy.pdf (44 pages, 6201260 bytes).
Transcript written on Scanpy.log.

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