Read the Docs build information
Build id: 1991139
Project: icb-scanpy-tutorials
Version: 77
Commit: 9d691cb85feb8510c46bf28b310d874524be96fc
Date: 2024-02-02T14:53:54.605955Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-02-02T14:53:55.736816Z, end-time: 2024-02-02T14:54:01.447928Z, duration: 5, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-02-02T14:54:01.520770Z, end-time: 2024-02-02T14:54:20.568359Z, duration: 19, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/77/head:external-77
From https://github.com/scverse/scanpy-tutorials
 * [new ref]         refs/pull/77/head -> external-77
 * [new tag]         1.4.6             -> 1.4.6

[rtd-command-info] start-time: 2024-02-02T14:54:20.697769Z, end-time: 2024-02-02T14:54:21.244881Z, duration: 0, exit-code: 0
git checkout --force 9d691cb85feb8510c46bf28b310d874524be96fc
Note: switching to '9d691cb85feb8510c46bf28b310d874524be96fc'.

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 9d691cb Fix ImplicitModificationWarning

[rtd-command-info] start-time: 2024-02-02T14:54:21.329396Z, end-time: 2024-02-02T14:54:21.387553Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2024-02-02T14:54:21.456923Z, end-time: 2024-02-02T14:54:21.519179Z, 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: 2024-02-02T14:54:27.558866Z, end-time: 2024-02-02T14:54:27.650481Z, duration: 0, exit-code: 0
asdf global python 3.11.6


[rtd-command-info] start-time: 2024-02-02T14:54:28.133337Z, end-time: 2024-02-02T14:54:29.200490Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.11.6.final.0-64 in 759ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/77, 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==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

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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/77/lib/python3.11/site-packages (23.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
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      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-23.3.2 setuptools-69.0.3

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python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.3 MarkupSafe-2.1.4 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.0

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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/77
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
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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.dev53+g9d691cb-py3-none-any.whl size=1038 sha256=672a17e0e87d91b5384d3b865e60314e6d40a8677454eee657881536807355d2
  Stored in directory: /tmp/pip-ephem-wheel-cache-ulqharvy/wheels/18/a9/b1/7317214a822bf3b8b3624faf133a2f82974977a859d2f7bf0f
Successfully built scanpy-tutorials
Installing collected packages: webencodings, wcwidth, pure-eval, ptyprocess, json5, fastjsonschema, widgetsnbextension, websocket-client, webcolors, uri-template, typing-extensions, types-python-dateutil, traitlets, tqdm, tornado, tinycss2, soupsieve, sniffio, six, send2trash, rpds-py, rfc3986-validator, rapidfuzz, pyzmq, pyyaml, python-json-logger, pyparsing, pycparser, psutil, prompt-toolkit, prometheus-client, platformdirs, pillow, pexpect, parso, pandocfilters, overrides, numpy, nest-asyncio, mistune, Mako, kiwisolver, jupyterlab-widgets, jupyterlab-pygments, jsonpointer, greenlet, fqdn, fonttools, executing, defusedxml, decorator, debugpy, cycler, attrs, async-lru, accessible-pygments, terminado, sqlalchemy, rfc3339-validator, referencing, python-dateutil, matplotlib-inline, jupyter-core, jedi, contourpy, comm, cffi, bleach, beautifulsoup4, asttokens, anyio, stack-data, pydata-sphinx-theme, matplotlib, jupyter-server-terminals, jupyter-client, jsonschema-specifications, arrow, argon2-cffi-bindings, alembic, sphinx-book-theme, jsonschema, isoduration, ipython, argon2-cffi, nbformat, ipywidgets, ipykernel, nbclient, jupyter-events, nbconvert, nbsphinx, jupyter-server, notebook-shim, jupyterlab-server, jupyter-lsp, jupyterlab, notebook, nbgrader, nbclean, scanpy-tutorials
Successfully installed Mako-1.3.2 accessible-pygments-0.0.4 alembic-1.13.1 anyio-4.2.0 argon2-cffi-23.1.0 argon2-cffi-bindings-21.2.0 arrow-1.3.0 asttokens-2.4.1 async-lru-2.0.4 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 cffi-1.16.0 comm-0.2.1 contourpy-1.2.0 cycler-0.12.1 debugpy-1.8.0 decorator-5.1.1 defusedxml-0.7.1 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.47.2 fqdn-1.5.1 greenlet-3.0.3 ipykernel-6.29.0 ipython-8.21.0 ipywidgets-8.1.1 isoduration-20.11.0 jedi-0.19.1 json5-0.9.14 jsonpointer-2.4 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyter-events-0.9.0 jupyter-lsp-2.2.2 jupyter-server-2.12.5 jupyter-server-terminals-0.5.2 jupyterlab-4.0.12 jupyterlab-pygments-0.3.0 jupyterlab-server-2.25.2 jupyterlab-widgets-3.0.9 kiwisolver-1.4.5 matplotlib-3.8.2 matplotlib-inline-0.1.6 mistune-3.0.2 nbclean-0.3.2 nbclient-0.9.0 nbconvert-7.14.2 nbformat-5.9.2 nbgrader-0.9.1 nbsphinx-0.9.3 nest-asyncio-1.6.0 notebook-7.0.7 notebook-shim-0.2.3 numpy-1.26.3 overrides-7.7.0 pandocfilters-1.5.1 parso-0.8.3 pexpect-4.9.0 pillow-10.2.0 platformdirs-4.2.0 prometheus-client-0.19.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pycparser-2.21 pydata-sphinx-theme-0.15.2 pyparsing-3.1.1 python-dateutil-2.8.2 python-json-logger-2.0.7 pyyaml-6.0.1 pyzmq-25.1.2 rapidfuzz-3.6.1 referencing-0.33.0 rfc3339-validator-0.1.4 rfc3986-validator-0.1.1 rpds-py-0.17.1 scanpy-tutorials-1.4.7.dev53+g9d691cb send2trash-1.8.2 six-1.16.0 sniffio-1.3.0 soupsieve-2.5 sphinx-book-theme-1.1.0 sqlalchemy-2.0.25 stack-data-0.6.3 terminado-0.18.0 tinycss2-1.2.1 tornado-6.4 tqdm-4.66.1 traitlets-5.14.1 types-python-dateutil-2.8.19.20240106 typing-extensions-4.9.0 uri-template-1.3.0 wcwidth-0.2.13 webcolors-1.13 webencodings-0.5.1 websocket-client-1.7.0 widgetsnbextension-4.0.9

[rtd-command-info] start-time: 2024-02-02T14:55:20.984891Z, end-time: 2024-02-02T14:55:21.046878Z, 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')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "77",
    'version_slug': "77",
    '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': '9d691cb85feb8510c46bf28b310d874524be96fc',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '9d691cb85feb8510c46bf28b310d874524be96fc',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '9d691cb85feb8510c46bf28b310d874524be96fc',
    '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': '9d691cb8',
}

# 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 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/scanpy-tutorials/pull/77'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-scanpy-tutorials/builds/1991139/'

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: 2024-02-02T14:55:21.119190Z, end-time: 2024-02-02T14:55:52.157818Z, duration: 31, exit-code: 0
python -m sphinx -T -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
making output directory... done
The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492
building [mo]: targets for 0 po files that are out of date
writing output... 
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/77/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... [ 55%] plotting/advanced
reading sources... [ 64%] plotting/core
reading sources... [ 73%] spatial/basic-analysis
reading sources... [ 82%] spatial/integration-scanorama
reading sources... [ 91%] tutorial_pearson_residuals
reading sources... [100%] visualizing-marker-genes
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/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/77/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/77/tutorial_pearson_residuals.ipynb: WARNING: document isn't included in any toctree
done
preparing documents... done
copying assets... copying static files... done
copying extra files... done
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... [ 55%] plotting/advanced
writing output... [ 64%] plotting/core
writing output... [ 73%] spatial/basic-analysis
writing output... [ 82%] spatial/integration-scanorama
writing output... [ 91%] tutorial_pearson_residuals
writing output... [100%] visualizing-marker-genes
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#customization'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#fig-ax'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#mpl-ax'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#size'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#gap'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#pretty-axes'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#legends'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#marks'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:13: WARNING: undefined label: '/plotting/advanced.ipynb#colors'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:14: WARNING: undefined label: '/plotting/advanced.ipynb#umap-subset'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:14: WARNING: undefined label: '/plotting/advanced.ipynb#umap-order'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:14: WARNING: undefined label: '/plotting/advanced.ipynb#umap-embed'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:14: WARNING: undefined label: '/plotting/advanced.ipynb#paga-prune'
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/77/plotting/advanced.ipynb:14: WARNING: undefined label: '/plotting/advanced.ipynb#paga-embed'
generating indices... genindex done
copying linked files... 
copying notebooks ... [ 12%] integrating-data-using-ingest.ipynb
copying notebooks ... [ 25%] paga-paul15.ipynb
copying notebooks ... [ 38%] pbmc3k.ipynb
copying notebooks ... [ 50%] plotting/advanced.ipynb
copying notebooks ... [ 62%] plotting/core.ipynb
copying notebooks ... [ 75%] spatial/basic-analysis.ipynb
copying notebooks ... [ 88%] spatial/integration-scanorama.ipynb
copying notebooks ... [100%] tutorial_pearson_residuals.ipynb
writing additional pages... search done
copying images... [  1%] _build/doctrees/nbsphinx/integrating-data-using-ingest_12_0.png
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