Read the Docs build information
Build id: 160094
Project: icb-scanpy
Version: latest
Commit: 66e64b40870035c3ee869e3baf34cf7110508d85
Date: 2018-11-16T09:17:27.002192Z
State: finished
Success: False


[rtd-command-info] start-time: 2018-11-16T15:17:27.460985Z, end-time: 2018-11-16T15:17:28.989464Z, duration: 1, exit-code: 0
git clone https://github.com/theislab/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2018-11-16T15:17:29.059939Z, end-time: 2018-11-16T15:17:29.158267Z, 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 66e64b4 Hook up leiden in tl and fix its docs

[rtd-command-info] start-time: 2018-11-16T15:17:29.226621Z, end-time: 2018-11-16T15:17:29.234142Z, duration: 0, exit-code: 0
git clean -d -f -f


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git branch -r
origin/HEAD -> origin/master
  origin/VolkerBergen-patch-1
  origin/hvg
  origin/kbet
  origin/master
  origin/norml
  origin/version0

[rtd-command-info] start-time: 2018-11-16T15:17:29.998353Z, end-time: 2018-11-16T15:17:32.773097Z, duration: 2, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.2'
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: 2018-11-16T15:17:32.837326Z, end-time: 2018-11-16T15:17:58.140595Z, duration: 25, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip Pygments==2.2.0 setuptools<40 docutils==0.13.1 mock==1.0.1 pillow==2.6.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.5.4 recommonmark==0.4.0 sphinx<1.8 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<0.6
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Building wheels for collected packages: mock, pillow, commonmark
  Running setup.py bdist_wheel for mock: started
  Running setup.py bdist_wheel for mock: finished with status 'done'
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  Running setup.py bdist_wheel for pillow: started
  Running setup.py bdist_wheel for pillow: finished with status 'done'
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  Running setup.py bdist_wheel for commonmark: started
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Successfully built mock pillow commonmark
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, imagesize, pytz, babel, six, snowballstemmer, certifi, chardet, urllib3, idna, requests, sphinxcontrib-websupport, MarkupSafe, Jinja2, pyparsing, packaging, sphinx, sphinx-rtd-theme, readthedocs-sphinx-ext
  Found existing installation: setuptools 39.0.1
    Uninstalling setuptools-39.0.1:
      Successfully uninstalled setuptools-39.0.1
Successfully installed Jinja2-2.10 MarkupSafe-1.1.0 Pygments-2.2.0 alabaster-0.7.12 babel-2.6.0 certifi-2018.10.15 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.7 imagesize-1.1.0 mock-1.0.1 packaging-18.0 pillow-2.6.1 pyparsing-2.3.0 pytz-2018.7 readthedocs-sphinx-ext-0.5.15 recommonmark-0.4.0 requests-2.20.1 setuptools-39.2.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.2 sphinxcontrib-websupport-1.1.0 urllib3-1.24.1
You are using pip version 9.0.3, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

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Requirement already satisfied: MarkupSafe>=0.23 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from Jinja2>=2.3->sphinx->sphinx_rtd_theme>=0.3.1->-r docs/requires.txt (line 2))
Requirement already satisfied: idna<2.8,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx->sphinx_rtd_theme>=0.3.1->-r docs/requires.txt (line 2))
Requirement already satisfied: chardet<3.1.0,>=3.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx->sphinx_rtd_theme>=0.3.1->-r docs/requires.txt (line 2))
Requirement already satisfied: urllib3<1.25,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx->sphinx_rtd_theme>=0.3.1->-r docs/requires.txt (line 2))
Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages (from requests>=2.0.0->sphinx->sphinx_rtd_theme>=0.3.1->-r docs/requires.txt (line 2))
Building wheels for collected packages: networkx
  Running setup.py bdist_wheel for networkx: started
  Running setup.py bdist_wheel for networkx: finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/68/f8/29/b53346a112a07d30a5a84d53f19aeadaa1a474897c0423af91
Successfully built networkx
Installing collected packages: sphinx-autodoc-typehints, natsort, numpy, scipy, h5py, python-dateutil, pandas, anndata, kiwisolver, cycler, matplotlib, seaborn, numexpr, tables, scikit-learn, decorator, networkx, joblib, llvmlite, numba
Successfully installed anndata-0.6.13 cycler-0.10.0 decorator-4.3.0 h5py-2.8.0 joblib-0.13.0 kiwisolver-1.0.1 llvmlite-0.25.0 matplotlib-3.0.2 natsort-5.4.1 networkx-2.2 numba-0.40.1 numexpr-2.6.8 numpy-1.15.4 pandas-0.23.4 python-dateutil-2.7.5 scikit-learn-0.20.0 scipy-1.1.0 seaborn-0.9.0 sphinx-autodoc-typehints-1.5.0 tables-3.4.4
You are using pip version 9.0.3, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-11-16T15:18:34.074818Z, end-time: 2018-11-16T15:18:34.140574Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
import inspect
import logging
from pathlib import Path
from datetime import datetime
from typing import Optional

from sphinx.application import Sphinx
from sphinx.ext import autosummary

# remove PyCharm’s old six module
if 'six' in sys.modules:
    print(*sys.path, sep='\n')
    for pypath in list(sys.path):
        if any(p in pypath for p in ['PyCharm', 'pycharm']) and 'helpers' in pypath:
            sys.path.remove(pypath)
    del sys.modules['six']

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.api  # noqa


logger = logging.getLogger(__name__)

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

needs_sphinx = '1.7'  # autosummary bugfix
extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.autosummary',
    # 'plot_generator',
    # 'plot_directive',
    'sphinx.ext.napoleon',
    'sphinx_autodoc_typehints',
    'sphinx.ext.intersphinx',
    # 'ipython_directive',
    # 'ipython_console_highlighting',
]

# Generate the API documentation when building
autosummary_generate = True
# both of the following two lines don't work
# see falexwolf's issue for numpydoc
# 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 = False
napoleon_custom_sections = [('Params', 'Parameters')]

intersphinx_mapping = dict(
    python=('https://docs.python.org/3', None),
    numpy=('https://docs.scipy.org/doc/numpy/', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    pandas=('http://pandas.pydata.org/pandas-docs/stable/', None),
    matplotlib=('https://matplotlib.org/', None),
    anndata=('https://anndata.readthedocs.io/en/latest/', None),
    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
)

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
project = 'Scanpy'
author = 'Alex Wolf, Philipp Angerer, Fidel Ramirez, Isaac Virshup, Davide Cittaro, Gokcen Eraslan, Tom White, Tobias Callies, Andrés R. Muñoz-Rojas.'
copyright = f'{datetime.now():%Y}, {author}'

version = scanpy.__version__.replace('.dirty', '')
release = version
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'
todo_include_todos = False


# -- Options for HTML output ----------------------------------------------

html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=2,
)
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']


def setup(app):
    app.add_stylesheet('css/custom.css')


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


htmlhelp_basename = 'Scanpydoc'
latex_documents = [
    (master_doc, 'Scanpy.tex', 'Scanpy Documentation',
     'Alex Wolf, Philipp Angerer', 'manual'),
]
man_pages = [
    (master_doc, 'scanpy', 'Scanpy Documentation',
     [author], 1)
]
texinfo_documents = [
    (master_doc, 'Scanpy', 'Scanpy Documentation',
     author, 'Scanpy', 'One line description of project.',
     'Miscellaneous'),
]


# -- generate_options override ------------------------------------------
# TODO: why?


def process_generate_options(app: Sphinx):
    genfiles = app.config.autosummary_generate

    if genfiles and not hasattr(genfiles, '__len__'):
        env = app.builder.env
        genfiles = [
            env.doc2path(x, base=None)
            for x in env.found_docs
            if Path(env.doc2path(x)).is_file()
        ]
    if not genfiles:
        return

    from sphinx.ext.autosummary.generate import generate_autosummary_docs

    ext = app.config.source_suffix
    genfiles = [
        genfile + (not genfile.endswith(tuple(ext)) and ext[0] or '')
        for genfile in genfiles
    ]

    suffix = autosummary.get_rst_suffix(app)
    if suffix is None:
        return

    generate_autosummary_docs(
        genfiles, builder=app.builder,
        warn=logger.warning, info=logger.info,
        suffix=suffix, base_path=app.srcdir,
        imported_members=True, app=app,
    )


autosummary.process_generate_options = process_generate_options


# -- GitHub URLs for class and method pages ------------------------------------------


def get_obj_module(qualname):
    """Get a module/class/attribute and its original module by qualname"""
    modname = qualname
    classname = None
    attrname = None
    while modname not in sys.modules:
        attrname = classname
        modname, classname = modname.rsplit('.', 1)

    # retrieve object and find original module name
    if classname:
        cls = getattr(sys.modules[modname], classname)
        modname = cls.__module__
        obj = getattr(cls, attrname) if attrname else cls
    else:
        obj = None

    return obj, sys.modules[modname]


def get_linenos(obj):
    """Get an object’s line numbers"""
    try:
        lines, start = inspect.getsourcelines(obj)
    except TypeError:
        return None, None
    else:
        return start, start + len(lines) - 1


project_dir = Path(__file__).parent.parent  # project/docs/conf.py/../.. → project/
github_url1 = 'https://github.com/{github_user}/{github_repo}/tree/{github_version}'.format_map(html_context)
github_url2 = 'https://github.com/theislab/anndata/tree/master'


def modurl(qualname: str) -> str:
    """Get the full GitHub URL for some object’s qualname."""
    obj, module = get_obj_module(qualname)
    github_url = github_url1
    try:
        path = Path(module.__file__).relative_to(project_dir)
    except ValueError:
        # trying to document something from another package
        github_url = github_url2
        path = '/'.join(module.__file__.split('/')[-2:])
    start, end = get_linenos(obj)
    fragment = f'#L{start}-L{end}' if start and end else ''
    return f'{github_url}/{path}{fragment}'


def api_image(qualname: str) -> Optional[str]:
    # I’d like to make this a contextfilter, but the jinja context doesn’t contain the path,
    # so no chance to not hardcode “api/” here.
    path = Path(__file__).parent / 'api' / f'{qualname}.png'
    print(path, path.is_file())
    return f'.. image:: {path.name}\n   :width: 200\n   :align: right' if path.is_file() else ''


# html_context doesn’t apply to autosummary templates ☹
# and there’s no way to insert filters into those templates
# so we have to modify the default filters
from jinja2.defaults import DEFAULT_FILTERS

DEFAULT_FILTERS.update(modurl=modurl, api_image=api_image)


# -- Override some classnames in autodoc --------------------------------------------


import sphinx_autodoc_typehints

qualname_overrides = {
    'anndata.base.AnnData': 'anndata.AnnData',
    'scipy.sparse.base.spmatrix': 'scipy.sparse.spmatrix',
    'scipy.sparse.csr.csr_matrix': 'scipy.sparse.csr_matrix',
    'scipy.sparse.csc.csc_matrix': 'scipy.sparse.csc_matrix',
}

fa_orig = sphinx_autodoc_typehints.format_annotation
def format_annotation(annotation):
    if inspect.isclass(annotation):
        full_name = '{}.{}'.format(annotation.__module__, annotation.__qualname__)
        override = qualname_overrides.get(full_name)
        if override is not None:
            return ':py:class:`~{}`'.format(qualname_overrides[full_name])
    return fa_orig(annotation)
sphinx_autodoc_typehints.format_annotation = format_annotation


# -- Prettier Param docs --------------------------------------------


from typing import Dict, List, Tuple

from docutils import nodes
from sphinx import addnodes
from sphinx.domains.python import PyTypedField, PyObject
from sphinx.environment import BuildEnvironment


class PrettyTypedField(PyTypedField):
    list_type = nodes.definition_list

    def make_field(
        self,
        types: Dict[str, List[nodes.Node]],
        domain: str,
        items: Tuple[str, List[nodes.inline]],
        env: BuildEnvironment = None
    ) -> nodes.field:
        def makerefs(rolename, name, node):
            return self.make_xrefs(rolename, domain, name, node, env=env)

        def handle_item(fieldarg: str, content: List[nodes.inline]) -> nodes.definition_list_item:
            head = nodes.term()
            head += makerefs(self.rolename, fieldarg, addnodes.literal_strong)
            fieldtype = types.pop(fieldarg, None)
            if fieldtype is not None:
                head += nodes.Text(' : ')
                if len(fieldtype) == 1 and isinstance(fieldtype[0], nodes.Text):
                    text_node, = fieldtype  # type: nodes.Text
                    head += makerefs(self.typerolename, text_node.astext(), addnodes.literal_emphasis)
                else:
                    head += fieldtype

            body_content = nodes.paragraph('', '', *content)
            body = nodes.definition('', body_content)

            return nodes.definition_list_item('', head, body)

        fieldname = nodes.field_name('', self.label)
        if len(items) == 1 and self.can_collapse:
            fieldarg, content = items[0]
            bodynode = handle_item(fieldarg, content)
        else:
            bodynode = self.list_type()
            for fieldarg, content in items:
                bodynode += handle_item(fieldarg, content)
        fieldbody = nodes.field_body('', bodynode)
        return nodes.field('', fieldname, fieldbody)


# replace matching field types with ours
PyObject.doc_field_types = [
    PrettyTypedField(
        ft.name,
        names=ft.names,
        typenames=ft.typenames,
        label=ft.label,
        rolename=ft.rolename,
        typerolename=ft.typerolename,
        can_collapse=ft.can_collapse,
    ) if isinstance(ft, PyTypedField) else ft
    for ft in PyObject.doc_field_types
]




###########################################################################
#          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
    else:
        SUFFIX = source_suffix[0]
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')
html_static_path.append('/home/docs/checkouts/readthedocs.org/readthedocs/templates/sphinx/_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/"),
    ],
    'downloads': [ 
    ("htmlzip", "//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/latest/',
    'analytics_code': '',
    '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': '66e64b40',
}




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"]

[rtd-command-info] start-time: 2018-11-16T15:18:34.203537Z, end-time: 2018-11-16T15:18:41.251301Z, duration: 7, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/bin
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python36.zip
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/lib-dynload
/home/docs/.pyenv/versions/3.6.2/lib/python3.6
/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages
loading translations [en]... done

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/cmdline.py", line 303, in main
    args.warningiserror, args.tags, args.verbosity, args.jobs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 191, in __init__
    self.setup_extension(extension)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 411, in setup_extension
    self.registry.load_extension(self, extname)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/registry.py", line 326, in load_extension
    metadata = mod.setup(app)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx_autodoc_typehints.py", line 228, in setup
    app.connect('config-inited', config_ready)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 427, in connect
    listener_id = self.events.connect(event, callback)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/events.py", line 63, in connect
    raise ExtensionError(__('Unknown event name: %s') % name)
sphinx.errors.ExtensionError: Unknown event name: config-inited

Extension error:
Unknown event name: config-inited