Read the Docs build information
Build id: 300379
Project: icb-scanpy
Version: latest
Commit: f963a7abf2c4aa3f9b7b2ee8691ba00c56110a3f
Date: 2020-03-11T06:57:08.379614Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-03-11T06:57:10.689076Z, end-time: 2020-03-11T06:57:14.246079Z, duration: 3, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-03-11T06:57:14.682652Z, end-time: 2020-03-11T06:57:14.994321Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: checking out '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 performing another checkout.

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

  git checkout -b <new-branch-name>

HEAD is now at f963a7a Test that loading an example visium dataset doesn't change results from another

[rtd-command-info] start-time: 2020-03-11T06:57:15.423292Z, end-time: 2020-03-11T06:57:15.636086Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-03-11T06:57:17.054254Z, end-time: 2020-03-11T06:57:21.701529Z, duration: 4, exit-code: 0
python3.6 -mvirtualenv  
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-03-11T06:57:21.861249Z, end-time: 2020-03-11T06:57:22.832804Z, duration: 0, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (20.0.2)

[rtd-command-info] start-time: 2020-03-11T06:57:23.012719Z, end-time: 2020-03-11T06:57:37.322012Z, duration: 14, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<1.1
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Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2019.11.28 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.6 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.0 urllib3-1.25.8

[rtd-command-info] start-time: 2020-03-11T06:57:37.484264Z, end-time: 2020-03-11T06:58:16.889767Z, duration: 39, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip -r docs/requirements.txt
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Successfully built umap-learn
Installing collected packages: numpy, scipy, zipp, importlib-metadata, h5py, python-dateutil, pandas, natsort, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, tqdm, joblib, scikit-learn, patsy, statsmodels, decorator, networkx, llvmlite, numba, umap-learn, get-version, legacy-api-wrap, setuptools-scm, sphinxcontrib-applehelp, sphinxcontrib-devhelp, sphinxcontrib-jsmath, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinx, sphinx-autodoc-typehints, scanpydoc, typing-extensions
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[rtd-command-info] start-time: 2020-03-11T06:58:18.239011Z, end-time: 2020-03-11T06:58:18.453582Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import warnings
from pathlib import Path
from datetime import datetime

import matplotlib  # noqa

# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / 'extensions')]
import scanpy  # noqa

on_rtd = os.environ.get('READTHEDOCS') == 'True'

# -- General configuration ------------------------------------------------


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = '2.0'  # Nicer param docs
suppress_warnings = ['ref.citation']

# General information
project = 'Scanpy'
author = scanpy.__author__
copyright = f'{datetime.now():%Y}, {author}.'
version = scanpy.__version__.replace('.dirty', '')
release = version

# default settings
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'

extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    # 'plot_generator',
    # 'plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    # 'ipython_directive',
    # 'ipython_console_highlighting',
    'scanpydoc',
    *[p.stem for p in (HERE / 'extensions').glob('*.py')],
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = 'bysource'
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [('Params', 'Parameters')]
todo_include_todos = False
api_dir = HERE / 'api'  # function_images

scanpy_tutorials_url = 'https://scanpy-tutorials.readthedocs.io/en/latest/'

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/stable/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    cycler=('https://matplotlib.org/cycler/', None),
    h5py=('http://docs.h5py.org/en/stable/', None),
    ipython=('https://ipython.readthedocs.io/en/stable/', None),
    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
    louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
    matplotlib=('https://matplotlib.org/', None),
    networkx=('https://networkx.github.io/documentation/networkx-1.10/', None),
    numpy=('https://docs.scipy.org/doc/numpy/', None),
    pandas=('https://pandas.pydata.org/pandas-docs/stable/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    scvelo=('https://scvelo.readthedocs.io/', None),
    seaborn=('https://seaborn.pydata.org/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=(scanpy_tutorials_url, None),
)


# -- 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',  # Repo name
    github_version='master',  # Version
    conf_py_path='/docs/',  # 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.warningiserror = on_rtd
    app.add_stylesheet('css/custom.css')


# -- Options for other output formats ------------------------------------------

htmlhelp_basename = f'{project}doc'
doc_title = f'{project} Documentation'
latex_documents = [(master_doc, f'{project}.tex', doc_title, author, 'manual')]
man_pages = [(master_doc, project, doc_title, [author], 1)]
texinfo_documents = [
    (
        master_doc,
        project,
        doc_title,
        author,
        project,
        'One line description of project.',
        'Miscellaneous',
    )
]


# -- Suppress link warnings ----------------------------------------------------

qualname_overrides = {
    "sklearn.neighbors.dist_metrics.DistanceMetric": "sklearn.neighbors.DistanceMetric",
    # If the docs are built with an old version of numpy, this will make it work:
    "numpy.random.RandomState": "numpy.random.mtrand.RandomState",
}

nitpick_ignore = [
    # Will probably be documented
    ('py:class', 'scanpy._settings.Verbosity'),
    # Currently undocumented: https://github.com/mwaskom/seaborn/issues/1810
    ('py:class', 'seaborn.ClusterGrid'),
    # Won’t be documented
    ('py:class', 'scanpy._utils.Empty'),
]




###########################################################################
#          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/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

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://media.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://media.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("1.4.4.post1", "/en/1.4.4.post1/"),
    ("1.1", "/en/1.1/"),
    ],
    'downloads': [ 
    ("html", "//icb-scanpy.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-scanpy.readthedocs-hosted.com/en/stable/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'proxied_api_host': '/_',
    'github_user': 'theislab',
    'github_repo': 'scanpy',
    '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,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'f963a7ab',
}




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")

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'

[rtd-command-info] start-time: 2020-03-11T06:58:18.612615Z, end-time: 2020-03-11T06:58:26.502934Z, duration: 7, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.4.4
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from http://docs.h5py.org/en/stable/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/objects.inv...
loading intersphinx inventory from https://networkx.github.io/documentation/networkx-1.10/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/numpy/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://docs.scipy.org/doc/scipy/reference/objects.inv...
loading intersphinx inventory from https://scvelo.readthedocs.io/objects.inv...
loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: _key_contributors.rst, _links.rst, api/index.rst, api/plotting.rst, api/scanpy.external.rst, api/scanpy.plotting.rst, basic_usage.rst, ecosystem.rst, external/index.rst, index.rst, installation.rst, references.rst, release-latest.rst, release-notes.rst, tutorials.rst, usage-principles.rst
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version.  The public classes are available in the top-level namespace.
  from pandas.core.index import RangeIndex
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest" is shallow and may cause errors
  warnings.warn('"{}" is shallow and may cause errors'.format(wd.path))

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/generate.py", line 272, in generate_autosummary_docs
    name, obj, parent, mod_name = import_by_name(name)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/__init__.py", line 599, in import_by_name
    raise ImportError('no module named %s' % ' or '.join(tried))
ImportError: no module named scanpy.external.pl.wishbone

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 275, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 278, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 334, in _init_builder
    self.events.emit('builder-inited')
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/events.py", line 99, in emit
    results.append(callback(self.app, *args))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/__init__.py", line 748, in process_generate_options
    app=app, imported_members=imported_members)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/ext/autosummary/generate.py", line 274, in generate_autosummary_docs
    _warn('[autosummary] failed to import %r: %s' % (name, e))
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1642, in warning
    self.log(WARNING, msg, *args, **kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 124, in log
    super().log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1674, in log
    self.logger.log(level, msg, *args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1374, in log
    self._log(level, msg, args, **kwargs)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1444, in _log
    self.handle(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1454, in handle
    self.callHandlers(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 1516, in callHandlers
    hdlr.handle(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 861, in handle
    rv = self.filter(record)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/logging/__init__.py", line 720, in filter
    result = f.filter(record)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/logging.py", line 406, in filter
    raise SphinxWarning(message)
sphinx.errors.SphinxWarning: [autosummary] failed to import 'scanpy.external.pl.wishbone': no module named scanpy.external.pl.wishbone

Warning, treated as error:
[autosummary] failed to import 'scanpy.external.pl.wishbone': no module named scanpy.external.pl.wishbone