Read the Docs build information
Build id: 1658839
Project: icb-scanpy-tutorials
Version: latest
Commit: e7ad0a920426f4a701a0b69c0d0f38c1c7523d78
Date: 2023-08-14T13:42:29.395931Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-08-14T13:42:33.361229Z, end-time: 2023-08-14T13:42:51.333711Z, duration: 17, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-08-14T13:42:51.620481Z, end-time: 2023-08-14T13:42:52.141839Z, 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 e7ad0a9 Fix project name

[rtd-command-info] start-time: 2023-08-14T13:42:52.590902Z, end-time: 2023-08-14T13:42:52.676436Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2023-08-14T13:42:52.927780Z, end-time: 2023-08-14T13:42:52.991563Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-22.04
  tools:
    python: "3.11"
sphinx:
  configuration: conf.py
python:
  install:
    - requirements: requirements.txt

[rtd-command-info] start-time: 2023-08-14T13:43:00.519680Z, end-time: 2023-08-14T13:43:00.642695Z, duration: 0, exit-code: 0
asdf global python 3.11.4


[rtd-command-info] start-time: 2023-08-14T13:43:01.274701Z, end-time: 2023-08-14T13:43:02.033191Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.4.final.0-64 in 444ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-08-14T13:43:02.280805Z, end-time: 2023-08-14T13:43:14.257257Z, duration: 11, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (21.2.3)
Collecting pip
  Downloading pip-23.2.1-py3-none-any.whl (2.1 MB)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages (57.4.0)
Collecting setuptools
  Downloading setuptools-68.0.0-py3-none-any.whl (804 kB)
Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 57.4.0
    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-23.2.1 setuptools-68.0.0

[rtd-command-info] start-time: 2023-08-14T13:43:14.471358Z, end-time: 2023-08-14T13:43:22.629920Z, duration: 8, exit-code: 0
python -m pip install --upgrade --no-cache-dir pillow 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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Building wheels for collected packages: mock
  Building wheel for mock (setup.py): started
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  Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23753 sha256=19fc79bd5de19a5fbb2f5a1bc13c3b078d8e88d895cc8fff45448d9e5509ba50
  Stored in directory: /tmp/pip-ephem-wheel-cache-3trurwz8/wheels/80/c2/c8/630c9eb889f0be0202cb11bf30b47aa54bf7588e8d50b70005
Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.7.22 charset-normalizer-3.2.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-10.0.0 readthedocs-sphinx-ext-2.2.2 recommonmark-0.5.0 requests-2.31.0 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 urllib3-2.0.4

[rtd-command-info] start-time: 2023-08-14T13:43:22.851934Z, end-time: 2023-08-14T13:43:53.694705Z, duration: 30, exit-code: 0
python -m pip install --exists-action=w --no-cache-dir -r requirements.txt
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Installing collected packages: y-py, webencodings, wcwidth, pure-eval, ptyprocess, pickleshare, json5, ipython-genutils, fastjsonschema, executing, backcall, widgetsnbextension, websocket-client, webcolors, uri-template, typing-extensions, traitlets, tqdm, tornado, tinycss2, soupsieve, sniffio, Send2Trash, rpds-py, rfc3986-validator, rfc3339-validator, rapidfuzz, pyzmq, pyyaml, python-json-logger, python-dateutil, pyparsing, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pexpect, parso, pandocfilters, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jupyter-ydoc, jsonpointer, greenlet, fqdn, fonttools, entrypoints, defusedxml, decorator, debugpy, cycler, bleach, attrs, asttokens, aiosqlite, aiofiles, ypy-websocket, terminado, stack-data, sqlalchemy, referencing, matplotlib-inline, jupyter-core, jedi, contourpy, comm, cffi, beautifulsoup4, arrow, anyio, matplotlib, jupyter-client, jsonschema-specifications, isoduration, ipython, argon2-cffi-bindings, alembic, jsonschema, ipywidgets, ipykernel, argon2-cffi, nbformat, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-server-fileid, nbclassic, jupyter-server-ydoc, notebook, jupyterlab, nbgrader, nbclean
Successfully installed Mako-1.2.4 Send2Trash-1.8.2 aiofiles-22.1.0 aiosqlite-0.19.0 alembic-1.11.2 anyio-3.7.1 argon2-cffi-21.3.0 argon2-cffi-bindings-21.2.0 arrow-1.2.3 asttokens-2.2.1 attrs-23.1.0 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 cffi-1.15.1 comm-0.1.4 contourpy-1.1.0 cycler-0.11.0 debugpy-1.6.7.post1 decorator-5.1.1 defusedxml-0.7.1 entrypoints-0.4 executing-1.2.0 fastjsonschema-2.18.0 fonttools-4.42.0 fqdn-1.5.1 greenlet-2.0.2 ipykernel-6.25.1 ipython-8.14.0 ipython-genutils-0.2.0 ipywidgets-8.1.0 isoduration-20.11.0 jedi-0.19.0 json5-0.9.14 jsonpointer-2.4 jsonschema-4.19.0 jsonschema-specifications-2023.7.1 jupyter-client-7.4.9 jupyter-core-5.3.1 jupyter-events-0.7.0 jupyter-server-1.24.0 jupyter-server-fileid-0.9.0 jupyter-server-ydoc-0.8.0 jupyter-ydoc-0.2.5 jupyterlab-3.6.5 jupyterlab-pygments-0.2.2 jupyterlab-server-2.24.0 jupyterlab-widgets-3.0.8 kiwisolver-1.4.4 matplotlib-3.7.2 matplotlib-inline-0.1.6 mistune-3.0.1 nbclassic-1.0.0 nbclean-0.3.2 nbclient-0.8.0 nbconvert-7.7.3 nbformat-5.9.2 nbgrader-0.8.4 nbsphinx-0.9.2 nest-asyncio-1.5.7 notebook-6.5.5 notebook-shim-0.2.3 numpy-1.25.2 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.10.0 prometheus-client-0.17.1 prompt-toolkit-3.0.39 psutil-5.9.5 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.21 pyparsing-3.0.9 python-dateutil-2.8.2 python-json-logger-2.0.7 pyyaml-6.0.1 pyzmq-24.0.1 rapidfuzz-3.2.0 referencing-0.30.2 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.9.2 sniffio-1.3.0 soupsieve-2.4.1 sqlalchemy-2.0.19 stack-data-0.6.2 terminado-0.17.1 tinycss2-1.2.1 tornado-6.3.3 tqdm-4.66.1 traitlets-5.9.0 typing-extensions-4.7.1 uri-template-1.3.0 wcwidth-0.2.6 webcolors-1.13 webencodings-0.5.1 websocket-client-1.6.1 widgetsnbextension-4.0.8 y-py-0.6.0 ypy-websocket-0.8.4

[rtd-command-info] start-time: 2023-08-14T13:43:57.298098Z, end-time: 2023-08-14T13:43:57.359489Z, duration: 0, exit-code: 0
cat conf.py
from datetime import datetime

project = 'scanpy-tutorials'
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': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy-tutorials',
    'name': u'scanpy-tutorials',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    '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': 'e7ad0a92',
}

# 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():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
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/1658839/'

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: 2023-08-14T13:43:57.620231Z, end-time: 2023-08-14T13:44:19.332877Z, duration: 21, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/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
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updating environment: 11 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.11/site-packages/nbsphinx/__init__.py:1058: RuntimeWarning: You are using an unsupported version of pandoc (2.9.2.1).
Your version must be at least (2.14.2) but less than (4.0.0).
Refer to https://pandoc.org/installing.html.
Continuing with doubts...
  nbconvert.utils.pandoc.check_pandoc_version()
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reading sources... [100%] visualizing-marker-genes

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/spatial/basic-analysis.ipynb:31: WARNING: Content block expected for the "note" directive; none found.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/spatial/integration-scanorama.ipynb:31: WARNING: Content block expected for the "note" directive; none found.
looking for now-outdated files... none found
pickling environment... done
checking consistency... /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
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writing output... [100%] visualizing-marker-genes

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#customization (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#fig-ax (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#mpl-ax (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#size (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#gap (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#pretty-axes (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#legends (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#marks (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: /plotting/advanced.ipynb#colors (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#umap-subset (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#umap-order (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#umap-embed (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#paga-prune (if the link has no caption the label must precede a section header)
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:14: WARNING: undefined label: /plotting/advanced.ipynb#paga-embed (if the link has no caption the label must precede a section header)
generating indices... genindex
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copying notebooks ... [ 87%] spatial/integration-scanorama.ipynb
copying notebooks ... [100%] tutorial_pearson_residuals.ipynb

writing additional pages... search
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build succeeded, 17 warnings.

The HTML pages are in _readthedocs/html.
Updating searchtools for Read the Docs search...