Read the Docs build information
Build id: 1666650
Project: icb-scanpy-tutorials
Version: latest
Commit: 3e4e43433830920af035675d1d9469a6d3918ec7
Date: 2023-08-17T14:23:03.097425Z
State: finished
Success: True


[rtd-command-info] start-time: 2023-08-17T14:23:11.647188Z, end-time: 2023-08-17T14:23:17.069132Z, duration: 5, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-08-17T14:23:17.524090Z, end-time: 2023-08-17T14:23:28.333414Z, duration: 10, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master
From https://github.com/scverse/scanpy-tutorials
 * [new tag]         1.4.5      -> 1.4.5
 * [new tag]         1.4.6      -> 1.4.6

[rtd-command-info] start-time: 2023-08-17T14:23:28.995965Z, end-time: 2023-08-17T14:23:29.174873Z, 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 3e4e434 switch to book theme (#75)

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git clean -d -f -f


[rtd-command-info] start-time: 2023-08-17T14:23:30.555680Z, end-time: 2023-08-17T14:23:30.640147Z, 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:
    - method: pip
      path: .

[rtd-command-info] start-time: 2023-08-17T14:23:38.837613Z, end-time: 2023-08-17T14:23:38.934326Z, duration: 0, exit-code: 0
asdf global python 3.11.4


[rtd-command-info] start-time: 2023-08-17T14:23:39.849092Z, end-time: 2023-08-17T14:23:40.743189Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.4.final.0-64 in 542ms
  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: 2023-08-17T14:23:41.264811Z, end-time: 2023-08-17T14:23:54.606665Z, duration: 13, 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)
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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
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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-68.1.0

[rtd-command-info] start-time: 2023-08-17T14:23:55.042885Z, end-time: 2023-08-17T14:24:02.943158Z, duration: 7, 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
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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: 2023-08-17T14:24:03.475188Z, end-time: 2023-08-17T14:24:40.360553Z, duration: 36, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest
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Building wheels for collected packages: scanpy-tutorials
  Building wheel for scanpy-tutorials (pyproject.toml): started
  Building wheel for scanpy-tutorials (pyproject.toml): finished with status 'done'
  Created wheel for scanpy-tutorials: filename=scanpy_tutorials-1.4.7.dev38+g3e4e434-py3-none-any.whl size=1719 sha256=4c7f35a5c848e8d42d1df9aaa33d3bc00f19fe8e1c2e6ef9a245590cadcabc55
  Stored in directory: /tmp/pip-ephem-wheel-cache-ktuvpg1o/wheels/ef/b4/ee/cfce9f20bbd116d554c1618aee8b098b68330da98eb3bebe42
Successfully built scanpy-tutorials
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, sphinxcontrib-jsmath, 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, accessible-pygments, 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, jupyter-server, notebook-shim, jupyterlab-server, jupyter-server-fileid, nbclassic, jupyter-server-ydoc, notebook, jupyterlab, nbgrader, nbclean, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx, pydata-sphinx-theme, sphinx-book-theme, nbsphinx, scanpy-tutorials
  Attempting uninstall: sphinx
    Found existing installation: Sphinx 1.8.6
    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
Successfully installed Mako-1.2.4 Send2Trash-1.8.2 accessible-pygments-0.0.4 aiofiles-22.1.0 aiosqlite-0.19.0 alembic-1.11.3 anyio-3.7.1 argon2-cffi-23.1.0 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-7.7.4 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 pydata-sphinx-theme-0.13.3 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 scanpy-tutorials-1.4.7.dev38+g3e4e434 sniffio-1.3.0 soupsieve-2.4.1 sphinx-5.3.0 sphinx-book-theme-1.0.1 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sqlalchemy-2.0.20 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: 2023-08-17T14:24:47.700844Z, end-time: 2023-08-17T14:24:47.757864Z, duration: 0, exit-code: 0
cat conf.py
from datetime import datetime
from pathlib import Path
from importlib.metadata import metadata

from nbclean import NotebookCleaner

meta = metadata('scanpy-tutorials')
project = meta['Name']
author = meta['Author']
copyright = f'{datetime.now():%Y}, {author}'
release = version = meta['Version']

extensions = [
    'nbsphinx',
]

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
language = 'en'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints', 'scanpy_workshop/*']
pygments_style = 'sphinx'

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

html_theme = 'sphinx_book_theme'
html_theme_options = dict( 
    repository_url='https://github.com/theislab/scanpy-tutorials',
    repository_branch='master',
    use_repository_button=True,
)
html_static_path = ['_static']
html_logo = '_static/img/Scanpy_Logo_BrightFG.svg'

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

for path in Path().rglob('**/*.ipynb'):
    ntbk = NotebookCleaner(str(path))
    ntbk.clear('stderr')
    ntbk.save(path)




###########################################################################
#          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': '3e4e4343',
}

# 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/1666650/'

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: 2023-08-17T14:24:48.295328Z, end-time: 2023-08-17T14:25:21.900689Z, duration: 33, exit-code: 0
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v5.3.0
making output directory... done
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 11 source files that are out of date
updating environment: [new config] 11 added, 0 changed, 0 removed
reading sources... [  9%] README
reading sources... [ 18%] index
reading sources... [ 27%] integrating-data-using-ingest
/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()
reading sources... [ 36%] paga-paul15
reading sources... [ 45%] pbmc3k
reading sources... [ 54%] plotting/advanced
reading sources... [ 63%] plotting/core
reading sources... [ 72%] spatial/basic-analysis
reading sources... [ 81%] spatial/integration-scanorama
reading sources... [ 90%] tutorial_pearson_residuals
reading sources... [100%] visualizing-marker-genes

/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/spatial/basic-analysis.ipynb:31: ERROR: 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: ERROR: 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
preparing documents... done
writing output... [  9%] README
writing output... [ 18%] index
writing output... [ 27%] integrating-data-using-ingest
writing output... [ 36%] paga-paul15
writing output... [ 45%] pbmc3k
writing output... [ 54%] plotting/advanced
writing output... [ 63%] plotting/core
writing output... [ 72%] spatial/basic-analysis
writing output... [ 81%] spatial/integration-scanorama
writing output... [ 90%] tutorial_pearson_residuals
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'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#fig-ax'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#mpl-ax'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#size'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#gap'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#pretty-axes'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/latest/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#legends'
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