Read the Docs build information
Build id: 904159
Project: icb-scanpy-tutorials
Version: latest
Commit: b52a0cf74d76506dd1a0cc542c4012f9a15ef021
Date: 2022-04-01T18:56:25.505395Z
State: finished
Success: True


[rtd-command-info] start-time: 2022-04-01T18:56:27.532187Z, end-time: 2022-04-01T18:56:36.743185Z, duration: 9, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2022-04-01T18:56:36.924111Z, end-time: 2022-04-01T18:56:37.467332Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 switching back to a branch.

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

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at b52a0cf Workshop updates (#52)

[rtd-command-info] start-time: 2022-04-01T18:56:37.666751Z, end-time: 2022-04-01T18:56:37.734832Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2022-04-01T18:56:38.891692Z, end-time: 2022-04-01T18:56:49.094354Z, duration: 10, exit-code: 0
python3.6 -mvirtualenv 
Using base prefix '/home/docs/.pyenv/versions/3.6.12'
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: 2022-04-01T18:56:49.259476Z, end-time: 2022-04-01T18:56:51.298806Z, duration: 2, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools<58.3.0
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    Uninstalling setuptools-59.6.0:
      Successfully uninstalled setuptools-59.6.0
Successfully installed setuptools-58.2.0

[rtd-command-info] start-time: 2022-04-01T18:56:51.520012Z, end-time: 2022-04-01T18:56:59.699917Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir 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<2.2 jinja2<3.1.0
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Building wheels for collected packages: mock, future
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  Stored in directory: /tmp/pip-ephem-wheel-cache-b27f_8nf/wheels/6e/9c/ed/4499c9865ac1002697793e0ae05ba6be33553d098f3347fb94
Successfully built mock future
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, requests, Pygments, packaging, jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock
Successfully installed MarkupSafe-2.0.1 Pygments-2.11.2 alabaster-0.7.12 babel-2.9.1 certifi-2021.10.8 charset-normalizer-2.0.12 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.3 imagesize-1.3.0 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.7 pytz-2022.1 readthedocs-sphinx-ext-2.1.5 recommonmark-0.5.0 requests-2.27.1 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.9

[rtd-command-info] start-time: 2022-04-01T18:56:59.868852Z, end-time: 2022-04-01T18:57:20.953317Z, duration: 21, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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  Downloading cffi-1.15.0-cp36-cp36m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (405 kB)
Collecting pycparser
  Downloading pycparser-2.21-py2.py3-none-any.whl (118 kB)
Building wheels for collected packages: nbgrader
  Building wheel for nbgrader (setup.py): started
  Building wheel for nbgrader (setup.py): finished with status 'done'
  Created wheel for nbgrader: filename=nbgrader-0.6.2-py3-none-any.whl size=13533292 sha256=ba7fd3fa41bf72ab1861558653fe4d8e20bf561463051b63756208c0bfe59520
  Stored in directory: /tmp/pip-ephem-wheel-cache-ba4pdynx/wheels/a9/1f/10/61a55303dc60be738a3f3d5da0812abf94405b5a9b5b09ed01
Successfully built nbgrader
Installing collected packages: zipp, typing-extensions, ipython-genutils, decorator, wcwidth, traitlets, pyrsistent, pycparser, ptyprocess, parso, importlib-metadata, attrs, webencodings, tornado, pyzmq, python-dateutil, prompt-toolkit, pickleshare, pexpect, nest-asyncio, jupyter-core, jsonschema, jedi, entrypoints, cffi, backcall, testpath, pandocfilters, nbformat, mistune, jupyter-client, ipython, defusedxml, dataclasses, bleach, argon2-cffi-bindings, terminado, Send2Trash, prometheus-client, nbconvert, ipykernel, argon2-cffi, notebook, widgetsnbextension, qtpy, jupyterlab-widgets, sqlalchemy, qtconsole, Mako, jupyter-console, jarowinkler, ipywidgets, importlib-resources, rapidfuzz, pillow, numpy, kiwisolver, jupyter, cycler, alembic, tqdm, nbgrader, matplotlib, nbsphinx, nbclean
  Attempting uninstall: pillow
    Found existing installation: Pillow 5.4.1
    Uninstalling Pillow-5.4.1:
      Successfully uninstalled Pillow-5.4.1
Successfully installed Mako-1.1.6 Send2Trash-1.8.0 alembic-1.7.7 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 attrs-21.4.0 backcall-0.2.0 bleach-4.1.0 cffi-1.15.0 cycler-0.11.0 dataclasses-0.8 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 importlib-metadata-4.8.3 importlib-resources-5.4.0 ipykernel-5.5.6 ipython-7.16.3 ipython-genutils-0.2.0 ipywidgets-7.7.0 jarowinkler-1.0.2 jedi-0.17.2 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-7.1.2 jupyter-console-6.4.3 jupyter-core-4.9.2 jupyterlab-widgets-1.1.0 kiwisolver-1.3.1 matplotlib-3.3.4 mistune-0.8.4 nbclean-0.3.2 nbconvert-5.6.1 nbformat-5.1.3 nbgrader-0.6.2 nbsphinx-0.8.8 nest-asyncio-1.5.4 notebook-6.4.10 numpy-1.19.5 pandocfilters-1.5.0 parso-0.7.1 pexpect-4.8.0 pickleshare-0.7.5 pillow-8.4.0 prometheus-client-0.13.1 prompt-toolkit-3.0.28 ptyprocess-0.7.0 pycparser-2.21 pyrsistent-0.18.0 python-dateutil-2.8.2 pyzmq-22.3.0 qtconsole-5.2.2 qtpy-2.0.1 rapidfuzz-2.0.7 sqlalchemy-1.3.24 terminado-0.12.1 testpath-0.6.0 tornado-6.1 tqdm-4.63.1 traitlets-4.3.3 typing-extensions-4.1.1 wcwidth-0.2.5 webencodings-0.5.1 widgetsnbextension-3.6.0 zipp-3.6.0

[rtd-command-info] start-time: 2022-04-01T18:57:22.323719Z, end-time: 2022-04-01T18:57:22.394100Z, 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', 'scanpy_workshop/*']
pygments_style = 'sphinx'

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

html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=4, 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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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://assets.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://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("multiomics", "/en/multiomics/"),
    ],
    'downloads': [ 
    ("html", "//scanpy-tutorials.readthedocs.io/_/downloads/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy-tutorials',
    'name': u'scanpy-tutorials',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://scanpy-tutorials.readthedocs.io/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    '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,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'b52a0cf7',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy-tutorials/builds/904159/'

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'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])

[rtd-command-info] start-time: 2022-04-01T18:57:22.559342Z, end-time: 2022-04-01T18:57:48.157246Z, duration: 25, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
Running Sphinx v1.8.6
loading translations [en]... done
making output directory...
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 13 source files that are out of date
updating environment: 13 added, 0 changed, 0 removed
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reading sources... [ 38%] index
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reading sources... [ 61%] pbmc3k
reading sources... [ 69%] plotting/core
reading sources... [ 76%] spatial/basic-analysis
reading sources... [ 84%] spatial/integration-scanorama
reading sources... [ 92%] tutorial_pearson_residuals
reading sources... [100%] visualizing-marker-genes

looking for now-outdated files... none found
pickling environment... done
checking consistency... /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/cite-seq/index.rst: WARNING: document isn't included in any toctree
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/tutorial_pearson_residuals.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
writing output... [  7%] README
writing output... [ 15%] cite-seq/index
writing output... [ 23%] cite-seq/pbmc5k
writing output... [ 30%] cite-seq/pbmc5k_alex
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writing output... [ 69%] plotting/core
writing output... [ 76%] spatial/basic-analysis
writing output... [ 84%] spatial/integration-scanorama
writing output... [ 92%] tutorial_pearson_residuals
writing output... [100%] visualizing-marker-genes

generating indices... genindex
copying notebooks ... [ 11%] cite-seq/pbmc5k.ipynb
copying notebooks ... [ 22%] cite-seq/pbmc5k_alex.ipynb
copying notebooks ... [ 33%] integrating-data-using-ingest.ipynb
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copying notebooks ... [ 88%] spatial/integration-scanorama.ipynb
copying notebooks ... [100%] tutorial_pearson_residuals.ipynb

writing additional pages... search
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[rtd-command-info] start-time: 2022-04-01T18:57:48.448300Z, end-time: 2022-04-01T18:58:12.102566Z, duration: 23, exit-code: 0
python -m sphinx -T -E -b readthedocssinglehtmllocalmedia -d _build/doctrees -D language=en . _build/localmedia
Running Sphinx v1.8.6
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build succeeded, 2 warnings.

The HTML page is in _build/localmedia.
Updating searchtools for Read the Docs search...