Read the Docs build information
Build id: 1439681
Project: icb-scanpy-tutorials
Version: latest
Commit: d42414ef924f6d7e5d3cda18cda344d8375894b4
Date: 2023-04-27T12:28:57.567218Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2023-04-27T12:28:59.540395Z, end-time: 2023-04-27T12:29:08.113729Z, duration: 8, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-04-27T12:29:08.302245Z, end-time: 2023-04-27T12:29:08.605022Z, 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 d42414e advanced plotting (#61)

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git clean -d -f -f


[rtd-command-info] start-time: 2023-04-27T12:29:10.058555Z, end-time: 2023-04-27T12:29:14.472584Z, duration: 4, exit-code: 0
python3.6 -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
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: 2023-04-27T12:29:14.655490Z, end-time: 2023-04-27T12:29:16.628304Z, duration: 1, 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: 2023-04-27T12:29:16.825689Z, end-time: 2023-04-27T12:29:24.539987Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow==5.4.1 mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23773 sha256=443474e813636bf686ef2565fd9b764c972e0196b6fd050cca985ecaac91ca5f
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Successfully built mock
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Successfully installed MarkupSafe-2.0.1 Pygments-2.14.0 alabaster-0.7.13 babel-2.11.0 certifi-2022.12.7 charset-normalizer-2.0.12 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-21.3 pillow-5.4.1 pyparsing-3.0.9 pytz-2023.3 readthedocs-sphinx-ext-2.2.0 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 urllib3-1.26.15

[rtd-command-info] start-time: 2023-04-27T12:29:24.746867Z, end-time: 2023-04-27T12:29:50.107269Z, duration: 25, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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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, ipywidgets, importlib-resources, rapidfuzz, pillow, numpy, kiwisolver, jupyter, cycler, alembic, tqdm, nbgrader, matplotlib, nbsphinx, nbclean
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[rtd-command-info] start-time: 2023-04-27T12:29:51.641919Z, end-time: 2023-04-27T12:29:51.704247Z, 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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
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",
    'proxied_static_path': "/_/static/",
    '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': 'd42414ef',
}

# 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/1439681/'

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'])