Read the Docs build information
Build id: 247813
Project: icb-scanpy
Version: latest
Commit: e46f89bf12ee5ea75c1e1064388dc43ff849840a
Date: 2019-10-07T10:11:56.270668Z
State: finished
Success: False


[rtd-command-info] start-time: 2019-10-07T10:11:56.735760Z, end-time: 2019-10-07T10:11:59.597294Z, 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: 2019-10-07T10:11:59.855882Z, end-time: 2019-10-07T10:11:59.954258Z, 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 e46f89b update bbknn reference (#861)

[rtd-command-info] start-time: 2019-10-07T10:12:00.100716Z, end-time: 2019-10-07T10:12:00.108547Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-10-07T10:12:01.106013Z, end-time: 2019-10-07T10:12:05.692645Z, 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/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: 2019-10-07T10:12:05.781359Z, end-time: 2019-10-07T10:12:08.389141Z, 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
  Downloading https://files.pythonhosted.org/packages/30/db/9e38760b32e3e7f40cce46dd5fb107b8c73840df38f0046d8e6514e675a1/pip-19.2.3-py2.py3-none-any.whl (1.4MB)
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-19.2.3

[rtd-command-info] start-time: 2019-10-07T10:12:08.479339Z, end-time: 2019-10-07T10:12:19.132494Z, duration: 10, exit-code: 0
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Successfully built mock future
Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, urllib3, certifi, idna, chardet, requests, snowballstemmer, MarkupSafe, Jinja2, six, imagesize, pytz, babel, pyparsing, packaging, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
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[rtd-command-info] start-time: 2019-10-07T10:12:19.211929Z, end-time: 2019-10-07T10:12:49.638703Z, duration: 30, 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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[rtd-command-info] start-time: 2019-10-07T10:12:50.399719Z, end-time: 2019-10-07T10:12:50.720657Z, 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.insert(0, str(HERE.parent))
import scanpy  # noqa

with warnings.catch_warnings():
    warnings.filterwarnings('ignore', category=FutureWarning)
    import scanpy.api

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

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


nitpicky = True  # Warn about broken links
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',
]

# 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/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/en/stable/', None),
    seaborn=('https://seaborn.pydata.org/', 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.warningiserror = on_rtd
    app.add_stylesheet('css/custom.css')
    app.connect('autodoc-process-docstring', insert_function_images)
    app.connect('build-finished', show_param_warnings)
    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


# -- Warn for non-annotated params ---------------------------------------------


_format_docutils_params_orig = NumpyDocstring._format_docutils_params
param_warnings = {}


def scanpy_log_param_types(self, fields, field_role='param', type_role='type'):
    for _name, _type, _desc in fields:
        if not _type:
            continue
        set_item = r"`'[a-z0-9_.-]+'`"
        if re.fullmatch(rf"{{{set_item}(, {set_item})*}}", _type):
            continue
        param_warnings.setdefault((self._name, self._obj), []).append(
            (_name, _type)
        )
    return _format_docutils_params_orig(self, fields, field_role, type_role)


def show_param_warnings(app, exception):
    import inspect

    for (fname, fun), params in param_warnings.items():
        _, line = inspect.getsourcelines(fun)
        file_name = inspect.getsourcefile(fun)
        params_str = '\n'.join(f'\t{n}: {t}' for n, t in params)
        warnings.warn_explicit(
            f'\nParameters in `{fname}` not set-like: {{`elm-1`, `s_el.2`}}.\n'
            'Convert to this format or replace with type annotations:\n'
            + params_str,
            UserWarning,
            file_name,
            line,
        )


NumpyDocstring._format_docutils_params = scanpy_log_param_types


# -- 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


# -- 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'),
]

for mod_name in [
    'pp',
    'tl',
    'pl',
    'queries',
    'logging',
    'datasets',
    'export_to',
    None,
]:
    if mod_name is None:
        mod = scanpy.api
        mod_name = 'scanpy.api'
    else:
        mod = getattr(scanpy.api, mod_name)
        mod_name = f'scanpy.api.{mod_name}'
    for name, item in vars(mod).items():
        if not callable(item):
            continue
        for kind in ['func', 'obj']:
            nitpick_ignore.append((f'py:{kind}', f'{mod_name}.{name}'))




###########################################################################
#          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/"),
    ("contributors", "/en/contributors/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-scanpy/downloads/htmlzip/latest/"),
    ],
    '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',
    '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': 'e46f89bf',
}




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: 2019-10-07T10:12:50.800427Z, end-time: 2019-10-07T10:13:05.404183Z, duration: 14, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.2.0
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/en/stable/objects.inv...
/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('"%s" is shallow and may cause errors' % (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/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 269, 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 330, 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 103, 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/intersphinx.py", line 228, in load_mappings
    "with the following issues:") + "\n" + issues)
  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: failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://scvelo.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://scvelo.readthedocs.io/en/stable/objects.inv

Warning, treated as error:
failed to reach any of the inventories with the following issues:
intersphinx inventory 'https://scvelo.readthedocs.io/en/stable/objects.inv' not fetchable due to <class 'requests.exceptions.HTTPError'>: 404 Client Error: Not Found for url: https://scvelo.readthedocs.io/en/stable/objects.inv