Read the Docs build information
Build id: 260890
Project: icb-scanpy
Version: stable
Commit: ec41b282450766ec41179895890aaae3f25b8a6c
Date: 2019-11-19T11:51:34.259592Z
State: finished
Success: True


[rtd-command-info] start-time: 2019-11-19T11:51:35.013001Z, end-time: 2019-11-19T11:51:37.480439Z, 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: 2019-11-19T11:51:37.760709Z, end-time: 2019-11-19T11:51:37.874760Z, duration: 0, exit-code: 0
git checkout --force origin/stable
Note: checking out 'origin/stable'.

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 ec41b28 updated reference in tutorials

[rtd-command-info] start-time: 2019-11-19T11:51:37.953909Z, end-time: 2019-11-19T11:51:37.969042Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-11-19T11:51:39.020463Z, end-time: 2019-11-19T11:51:43.861827Z, duration: 4, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
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: 2019-11-19T11:51:43.955832Z, end-time: 2019-11-19T11:51:46.618425Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip pip
Collecting pip
  Using cached https://files.pythonhosted.org/packages/00/b6/9cfa56b4081ad13874b0c6f96af8ce16cfbc1cb06bedf8e9164ce5551ec1/pip-19.3.1-py2.py3-none-any.whl
Installing collected packages: pip
  Found existing installation: pip 19.1.1
    Uninstalling pip-19.1.1:
      Successfully uninstalled pip-19.1.1
Successfully installed pip-19.3.1

[rtd-command-info] start-time: 2019-11-19T11:51:46.694348Z, end-time: 2019-11-19T11:51:58.017035Z, duration: 11, exit-code: 0
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Requirement already up-to-date: setuptools==41.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (41.0.1)
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[rtd-command-info] start-time: 2019-11-19T11:51:58.102051Z, end-time: 2019-11-19T11:52:30.865542Z, duration: 32, 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
Requirement already satisfied: sphinx_rtd_theme>=0.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from -r docs/requirements.txt (line 2)) (0.4.3)
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Collecting llvmlite>=0.30.0dev0
  Using cached https://files.pythonhosted.org/packages/b3/93/924788871a889ead1c115ba2d43e67932a8865d38fdb179505c99e4bb575/llvmlite-0.30.0-cp36-cp36m-manylinux1_x86_64.whl
Collecting zipp>=0.5
  Using cached https://files.pythonhosted.org/packages/74/3d/1ee25a26411ba0401b43c6376d2316a71addcc72ef8690b101b4ea56d76a/zipp-0.6.0-py2.py3-none-any.whl
Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.1.1)
Requirement already satisfied: urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (1.25.7)
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2019.9.11)
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (3.0.4)
Requirement already satisfied: idna<2.9,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/stable/lib/python3.6/site-packages (from requests>=2.5.0->sphinx>=2.0.1->-r docs/requirements.txt (line 5)) (2.8)
Collecting more-itertools
  Using cached https://files.pythonhosted.org/packages/45/dc/3241eef99eb45f1def35cf93af35d1cf9ef4c0991792583b8f33ea41b092/more_itertools-7.2.0-py3-none-any.whl
Installing collected packages: sphinxcontrib-applehelp, sphinxcontrib-devhelp, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinxcontrib-jsmath, sphinxcontrib-qthelp, sphinx, sphinx-autodoc-typehints, get-version, scanpydoc, numpy, h5py, scipy, natsort, python-dateutil, pandas, anndata, cycler, kiwisolver, matplotlib, seaborn, numexpr, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, more-itertools, zipp, importlib-metadata, umap-learn
  Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
Successfully installed anndata-0.6.22.post1 cycler-0.10.0 decorator-4.4.1 get-version-2.1 h5py-2.10.0 importlib-metadata-0.23 joblib-0.14.0 kiwisolver-1.1.0 llvmlite-0.30.0 matplotlib-3.1.1 more-itertools-7.2.0 natsort-6.2.0 networkx-2.4 numba-0.46.0 numexpr-2.7.0 numpy-1.17.4 pandas-0.25.3 python-dateutil-2.8.1 scanpydoc-0.4.4 scikit-learn-0.21.3 scipy-1.3.2 seaborn-0.9.0 sphinx-2.2.1 sphinx-autodoc-typehints-1.10.3 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 tables-3.6.1 tqdm-4.38.0 umap-learn-0.3.10 zipp-0.6.0

[rtd-command-info] start-time: 2019-11-19T11:52:33.383795Z, end-time: 2019-11-19T11:52:33.697186Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
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.insert(0, str(HERE.parent))
import scanpy  # noqa


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


needs_sphinx = '1.7'  # autosummary bugfix

# 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',
]

# 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

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/latest/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', 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=('http://pandas.pydata.org/pandas-docs/stable/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', 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_RGB.png'
gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context)


def setup(app):
    app.add_stylesheet('css/custom.css')
    app.connect('autodoc-process-docstring', insert_function_images)
    app.add_role('pr', autolink(f'{gh_url}/pull/{{}}', 'PR {}'))


# -- 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'),
]


# -- Images for plot functions -------------------------------------------------


def insert_function_images(app, what, name, obj, options, lines):
    path = Path(__file__).parent / 'api' / f'{name}.png'
    if what != 'function' or not path.is_file(): return
    lines[0:0] = [f'.. image:: {path.name}', '   :width: 200', '   :align: right', '']


# -- GitHub links --------------------------------------------------------------


def autolink(url_template, title_template='{}'):
    from docutils import nodes
    def role(name, rawtext, text, lineno, inliner, options={}, content=[]):
        url = url_template.format(text)
        title = title_template.format(text)
        node = nodes.reference(rawtext, title, refuri=url, **options)
        return [node], []
    return role


# -- Test for new scanpydoc functionality --------------------------------------


import re
from sphinx.ext.napoleon import NumpyDocstring


def process_return(lines):
    for line in lines:
        m = re.fullmatch(r'(?P<param>\w+)\s+:\s+(?P<type>[\w.]+)', line)
        if m:
            # Once this is in scanpydoc, we can use the fancy hover stuff
            yield f'**{m["param"]}** : :class:`~{m["type"]}`'
        else:
            yield line


def scanpy_parse_returns_section(self, section):
    lines_raw = list(process_return(self._dedent(self._consume_to_next_section())))
    lines = self._format_block(':returns: ', lines_raw)
    if lines and lines[-1]:
        lines.append('')
    return lines


NumpyDocstring._parse_returns_section = scanpy_parse_returns_section


# -- Debug code ----------------------------------------------------------------


# Just do the following to see the rst of a function:
# rm -f _build/doctrees/api/scanpy.<what_you_want>.doctree; DEBUG=1 make html
import os
if os.environ.get('DEBUG') is not None:
    import sphinx.ext.napoleon
    pd = sphinx.ext.napoleon._process_docstring
    def pd_new(app, what, name, obj, options, lines):
        pd(app, what, name, obj, options, lines)
        print(*lines, sep='\n')
    sphinx.ext.napoleon._process_docstring = pd_new




###########################################################################
#          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/"),
    ("inherit-requirements", "/en/inherit-requirements/"),
    ("contributors", "/en/contributors/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/stable/"),
    ],
    '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': 'https://readthedocs.org',
    'github_user': 'theislab',
    'github_repo': 'scanpy',
    'github_version': 'stable',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'stable',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'stable',
    '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': 'ec41b282',
}




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: 2019-11-19T11:52:33.799852Z, end-time: 2019-11-19T11:53:59.917053Z, duration: 86, exit-code: 0
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.2.1
loading translations [en]... done
making output directory... done
loading intersphinx inventory from https://anndata.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/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 http://pandas.pydata.org/pandas-docs/stable/objects.inv...
intersphinx inventory has moved: http://pandas.pydata.org/pandas-docs/stable/objects.inv -> 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://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: api/index.rst, api/plotting.rst, api/scanpy.api.rst, api/scanpy.plotting.rst, basic_usage.rst, examples.rst, external/index.rst, index.rst, installation.rst, references.rst, release_notes.rst, tutorials.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.api.Neighbors.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.blobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.krumsiek11.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.moignard15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.paul15.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.pbmc3k.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.pbmc68k_reduced.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.datasets.toggleswitch.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.pl.phate.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/external/scanpy.external.pp.bbknn.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.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
[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.api.Neighbors.connectivities.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.distances.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.distances_dpt.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.eigen_basis.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.eigen_values.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.getdoc.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.rp_forest.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.to_igraph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.transitions.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.api.Neighbors.transitions_sym.rst
building [mo]: targets for 0 po files that are out of date
building [readthedocs]: targets for 12 source files that are out of date
updating environment: [new config] 219 added, 0 changed, 0 removed
reading sources... [  0%] api/index
reading sources... [  0%] api/plotting
reading sources... [  1%] api/scanpy.Neighbors
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:6: FutureWarning: 

In a future version of Scanpy, `scanpy.api` will be removed.
Simply use `import scanpy as sc` and `import scanpy.external as sce` instead.

  FutureWarning
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst:2: WARNING: duplicate object description of scanpy, other instance in api/index, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/__init__.py:docstring of scanpy:1: WARNING: Duplicate ID: "module-scanpy".
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:docstring of scanpy.api:209: WARNING: duplicate label settings, other instance in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/index.rst
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/api/scanpy.plotting.rst:2: WARNING: duplicate object description of scanpy, other instance in api/index, use :noindex: for one of them
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_total:39: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_total:43: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/preprocessing/_normalization.py:docstring of scanpy.pp.normalize_total:46: WARNING: Bullet list ends without a blank line; unexpected unindent.
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/external/_tools/_palantir.py:docstring of scanpy.external.tl.palantir:114: WARNING: Bullet list ends without a blank line; unexpected unindent.
release_notes.rst:24: WARNING: Title underline too short.

Post v1.4 :small:`July 20, 2019`
-------------------------------
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/release_notes.rst:24: WARNING: Title underline too short.

Post v1.4 :small:`July 20, 2019`
-------------------------------
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:32: WARNING: Citation [Ester96] is not referenced.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/docs/references.rst:90: WARNING: Citation [Krumsiek10] is not referenced.
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/stable/scanpy/api/__init__.py:6: FutureWarning: 

In a future version of Scanpy, `scanpy.api` will be removed.
Simply use `import scanpy as sc` and `import scanpy.external as sce` instead.

  FutureWarning
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Post v1.4 :small:`July 20, 2019`
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Post v1.4 :small:`July 20, 2019`
-------------------------------
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assembling single document... tutorials basic_usage installation api/index api/scanpy.pp.calculate_qc_metrics api/scanpy.pp.filter_cells api/scanpy.pp.filter_genes api/scanpy.pp.highly_variable_genes api/scanpy.pp.log1p api/scanpy.pp.pca api/scanpy.pp.normalize_total api/scanpy.pp.regress_out api/scanpy.pp.scale api/scanpy.pp.subsample api/scanpy.pp.downsample_counts api/scanpy.pp.recipe_zheng17 api/scanpy.pp.recipe_weinreb17 api/scanpy.pp.recipe_seurat api/scanpy.pp.combat api/scanpy.pp.neighbors api/scanpy.tl.pca api/scanpy.tl.tsne api/scanpy.tl.umap api/scanpy.tl.draw_graph api/scanpy.tl.diffmap api/scanpy.tl.leiden api/scanpy.tl.louvain api/scanpy.tl.dendrogram api/scanpy.tl.dpt api/scanpy.tl.paga api/scanpy.tl.rank_genes_groups api/scanpy.tl.filter_rank_genes_groups api/scanpy.tl.marker_gene_overlap api/scanpy.tl.score_genes api/scanpy.tl.score_genes_cell_cycle api/scanpy.tl.sim api/scanpy.plotting api/scanpy.pl.scatter api/scanpy.pl.heatmap api/scanpy.pl.dotplot api/scanpy.pl.violin api/scanpy.pl.stacked_violin api/scanpy.pl.matrixplot api/scanpy.pl.clustermap api/scanpy.pl.ranking api/scanpy.pl.highest_expr_genes api/scanpy.pl.filter_genes_dispersion api/scanpy.pl.highly_variable_genes api/scanpy.pl.pca api/scanpy.pl.pca_loadings api/scanpy.pl.pca_variance_ratio api/scanpy.pl.pca_overview api/scanpy.pl.tsne api/scanpy.pl.umap api/scanpy.pl.diffmap api/scanpy.pl.draw_graph api/scanpy.pl.embedding_density api/scanpy.pl.dpt_groups_pseudotime api/scanpy.pl.dpt_timeseries api/scanpy.pl.paga api/scanpy.pl.paga_path api/scanpy.pl.paga_compare api/scanpy.pl.rank_genes_groups api/scanpy.pl.rank_genes_groups_violin api/scanpy.pl.rank_genes_groups_stacked_violin api/scanpy.pl.rank_genes_groups_heatmap api/scanpy.pl.rank_genes_groups_dotplot api/scanpy.pl.rank_genes_groups_matrixplot api/scanpy.pl.sim api/scanpy.read api/scanpy.read_10x_h5 api/scanpy.read_10x_mtx api/scanpy.read_h5ad api/scanpy.read_csv api/scanpy.read_excel api/scanpy.read_hdf api/scanpy.read_loom api/scanpy.read_mtx api/scanpy.read_text api/scanpy.read_umi_tools api/scanpy.get.obs_df api/scanpy.get.var_df api/scanpy.get.rank_genes_groups_df api/scanpy.queries.mitochondrial_genes api/scanpy.Neighbors api/scanpy.Neighbors.connectivities api/scanpy.Neighbors.distances api/scanpy.Neighbors.distances_dpt api/scanpy.Neighbors.eigen_basis api/scanpy.Neighbors.eigen_values api/scanpy.Neighbors.getdoc api/scanpy.Neighbors.rp_forest api/scanpy.Neighbors.transitions api/scanpy.Neighbors.transitions_sym api/scanpy.Neighbors.compute_eigen api/scanpy.Neighbors.compute_neighbors api/scanpy.Neighbors.compute_transitions api/scanpy.Neighbors.to_igraph api/scanpy.set_figure_params api/scanpy._settings.ScanpyConfig api/scanpy._settings.ScanpyConfig.autosave api/scanpy._settings.ScanpyConfig.autoshow api/scanpy._settings.ScanpyConfig.cachedir api/scanpy._settings.ScanpyConfig.categories_to_ignore api/scanpy._settings.ScanpyConfig.datasetdir api/scanpy._settings.ScanpyConfig.figdir api/scanpy._settings.ScanpyConfig.file_format_data api/scanpy._settings.ScanpyConfig.file_format_figs api/scanpy._settings.ScanpyConfig.getdoc api/scanpy._settings.ScanpyConfig.logfile api/scanpy._settings.ScanpyConfig.logpath api/scanpy._settings.ScanpyConfig.max_memory api/scanpy._settings.ScanpyConfig.n_jobs api/scanpy._settings.ScanpyConfig.plot_suffix api/scanpy._settings.ScanpyConfig.verbosity api/scanpy._settings.ScanpyConfig.writedir api/scanpy._settings.ScanpyConfig.set_figure_params api/scanpy.logging.print_versions api/scanpy.datasets.blobs api/scanpy.datasets.ebi_expression_atlas api/scanpy.datasets.krumsiek11 api/scanpy.datasets.moignard15 api/scanpy.datasets.pbmc3k api/scanpy.datasets.pbmc68k_reduced api/scanpy.datasets.paul15 api/scanpy.datasets.toggleswitch api/scanpy.api api/scanpy.api.pp.calculate_qc_metrics api/scanpy.api.pp.filter_cells api/scanpy.api.pp.filter_genes api/scanpy.api.pp.highly_variable_genes api/scanpy.api.pp.filter_genes_dispersion api/scanpy.api.pp.log1p api/scanpy.api.pp.pca api/scanpy.api.pp.normalize_per_cell api/scanpy.api.pp.regress_out api/scanpy.api.pp.scale api/scanpy.api.pp.subsample api/scanpy.api.pp.downsample_counts api/scanpy.api.pp.recipe_zheng17 api/scanpy.api.pp.recipe_weinreb17 api/scanpy.api.pp.recipe_seurat api/scanpy.api.pp.bbknn api/scanpy.api.pp.mnn_correct api/scanpy.api.pp.dca api/scanpy.api.pp.magic api/scanpy.api.pp.neighbors api/scanpy.api.tl.pca api/scanpy.api.tl.tsne api/scanpy.api.tl.umap api/scanpy.api.tl.draw_graph api/scanpy.api.tl.diffmap api/scanpy.api.tl.phate api/scanpy.api.tl.leiden api/scanpy.api.tl.louvain api/scanpy.api.tl.dpt api/scanpy.api.tl.paga api/scanpy.api.tl.rank_genes_groups api/scanpy.api.tl.score_genes api/scanpy.api.tl.score_genes_cell_cycle api/scanpy.api.tl.sandbag api/scanpy.api.tl.cyclone api/scanpy.api.tl.sim api/scanpy.api.read api/scanpy.api.read_10x_h5 api/scanpy.api.read_10x_mtx api/scanpy.api.read_h5ad api/scanpy.api.read_csv api/scanpy.api.read_excel api/scanpy.api.read_hdf api/scanpy.api.read_loom api/scanpy.api.read_mtx api/scanpy.api.read_text api/scanpy.api.read_umi_tools api/scanpy.api.queries.mitochondrial_genes api/scanpy.api.Neighbors api/scanpy.api.Neighbors.connectivities api/scanpy.api.Neighbors.distances api/scanpy.api.Neighbors.distances_dpt api/scanpy.api.Neighbors.eigen_basis api/scanpy.api.Neighbors.eigen_values api/scanpy.api.Neighbors.getdoc api/scanpy.api.Neighbors.rp_forest api/scanpy.api.Neighbors.transitions api/scanpy.api.Neighbors.transitions_sym api/scanpy.api.Neighbors.compute_eigen api/scanpy.api.Neighbors.compute_neighbors api/scanpy.api.Neighbors.compute_transitions api/scanpy.api.Neighbors.to_igraph api/scanpy.api.set_figure_params api/scanpy.api.logging.print_versions api/scanpy.api.datasets.blobs api/scanpy.api.datasets.krumsiek11 api/scanpy.api.datasets.moignard15 api/scanpy.api.datasets.pbmc3k api/scanpy.api.datasets.pbmc68k_reduced api/scanpy.api.datasets.paul15 api/scanpy.api.datasets.toggleswitch api/scanpy.api.export_to.spring_project api/scanpy.pp.filter_genes_dispersion api/scanpy.pp.normalize_per_cell external/index external/scanpy.external.pp.bbknn external/scanpy.external.pp.mnn_correct external/scanpy.external.pp.dca external/scanpy.external.pp.magic external/scanpy.external.tl.phate external/scanpy.external.tl.palantir external/scanpy.external.tl.phenograph external/scanpy.external.tl.sandbag external/scanpy.external.tl.cyclone external/scanpy.external.pl.phate external/scanpy.external.exporting.spring_project external/scanpy.external.exporting.cellbrowser references done
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