Read the Docs build information
Build id: 288476
Project: icb-scanpy
Version: stable
Commit: e516b03120ec4649604379b7507617d176e10b62
Date: 2020-02-13T14:46:06.518915Z
State: finished
Success: False


[rtd-command-info] start-time: 2020-02-13T14:46:08.835106Z, end-time: 2020-02-13T14:46:11.734515Z, duration: 2, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2020-02-13T14:46:11.988097Z, end-time: 2020-02-13T14:46:12.315821Z, duration: 0, exit-code: 0
git checkout --force e516b03120ec4649604379b7507617d176e10b62
Note: checking out 'e516b03120ec4649604379b7507617d176e10b62'.

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 e516b03 make sure the newest umap is used in a test (#1042)

[rtd-command-info] start-time: 2020-02-13T14:46:12.375799Z, end-time: 2020-02-13T14:46:12.599837Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2020-02-13T14:46:13.951777Z, end-time: 2020-02-13T14:46:19.611594Z, duration: 5, exit-code: 0
python3.6 -mvirtualenv --no-site-packages 
Using base prefix '/home/docs/.pyenv/versions/3.6.8'
New python executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2020-02-13T14:46:19.673997Z, end-time: 2020-02-13T14:46:20.731443Z, duration: 1, 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/stable/lib/python3.6/site-packages (20.0.2)

[rtd-command-info] start-time: 2020-02-13T14:46:20.798185Z, end-time: 2020-02-13T14:46:32.283573Z, duration: 11, 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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Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, imagesize, six, MarkupSafe, Jinja2, snowballstemmer, pyparsing, packaging, sphinxcontrib-websupport, pytz, babel, chardet, idna, urllib3, certifi, requests, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
  Attempting uninstall: setuptools
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[rtd-command-info] start-time: 2020-02-13T14:46:32.345071Z, end-time: 2020-02-13T14:47:12.180850Z, 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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Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/1b/69/69/91e19c0578b1740a6358f5db2c2dcc5af5b04360c3c9066b26/umap_learn-0.3.10-py3-none-any.whl
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Installing collected packages: numpy, h5py, scipy, python-dateutil, pandas, natsort, zipp, importlib-metadata, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, tables, tqdm, joblib, scikit-learn, patsy, statsmodels, decorator, networkx, llvmlite, numba, umap-learn, get-version, legacy-api-wrap, setuptools-scm, sphinxcontrib-jsmath, sphinxcontrib-applehelp, sphinxcontrib-qthelp, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinx, sphinx-autodoc-typehints, scanpydoc, typing-extensions
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[rtd-command-info] start-time: 2020-02-13T14:47:13.088673Z, end-time: 2020-02-13T14:47:13.347187Z, 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"
}

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.readwrite.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': "stable",
    'version_slug': "stable",
    '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/"),
    ("spatial", "/en/spatial/"),
    ],
    'downloads': [ 
    ("html", "//icb-scanpy.readthedocs-hosted.com/_/downloads/en/stable/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': 'e516b03120ec4649604379b7507617d176e10b62',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'e516b03120ec4649604379b7507617d176e10b62',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'e516b03120ec4649604379b7507617d176e10b62',
    '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': 'e516b031',
}




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: 2020-02-13T14:47:13.415078Z, end-time: 2020-02-13T14:49:45.076591Z, duration: 151, exit-code: 2
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.4.1
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...
intersphinx inventory has moved: https://docs.scipy.org/doc/numpy/objects.inv -> https://numpy.org/doc/1.18/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
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.ebi_expression_atlas.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.pbmc3k_processed.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.datasets.pbmc68k_reduced.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.pp.dca.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.pp.magic.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.pp.mnn_correct.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.cyclone.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.harmony_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.palantir.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.phenograph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.sandbag.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.tl.trimap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.compute_eigen.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.compute_neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.compute_transitions.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.connectivities.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.distances.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.distances_dpt.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.eigen_basis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.eigen_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.Neighbors.rp_forest.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy._settings.ScanpyConfig.writedir.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 16 source files that are out of date
updating environment: [new config] 164 added, 0 changed, 0 removed
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/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/stable/lib/python3.6/site-packages/setuptools_scm/git.py:68: UserWarning: "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable" 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/stable/lib/python3.6/site-packages/sphinx/cmd/build.py", line 276, in build_main
    app.build(args.force_all, filenames)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/application.py", line 349, in build
    self.builder.build_update()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 299, in build_update
    len(to_build))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 361, in build
    self.write(docnames, list(updated_docnames), method)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 535, in write
    self._write_serial(sorted(docnames))
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/builders/__init__.py", line 545, in _write_serial
    self.write_doc(docname, doctree)
  File "/home/docs/.pyenv/versions/3.6.8/lib/python3.6/contextlib.py", line 88, in __exit__
    next(self.gen)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/logging.py", line 219, in pending_warnings
    memhandler.flushTo(logger)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages/sphinx/util/logging.py", line 184, in flushTo
    logger.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/stable/lib/python3.6/site-packages/sphinx/util/logging.py", line 404, in filter
    raise SphinxWarning(location + ":" + message)
sphinx.errors.SphinxWarning: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/preprocessing/_simple.py:docstring of scanpy.pp.downsample_counts:17:py:class reference target not found: numpy.random.mtrand.RandomState

Warning, treated as error:
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/preprocessing/_simple.py:docstring of scanpy.pp.downsample_counts:17:py:class reference target not found: numpy.random.mtrand.RandomState