Read the Docs build information
Build id: 236272
Project: icb-anndata
Version: latest
Commit: 926b82d9144a61bab4aa3c6ef0848d256b39c3bf
Date: 2019-08-27T09:29:40.078056Z
State: finished
Success: False


[rtd-command-info] start-time: 2019-08-27T09:29:40.578978Z, end-time: 2019-08-27T09:29:41.121380Z, duration: 0, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/theislab/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2019-08-27T09:29:41.405015Z, end-time: 2019-08-27T09:29:41.415664Z, 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 926b82d Fixed some links

[rtd-command-info] start-time: 2019-08-27T09:29:41.512927Z, end-time: 2019-08-27T09:29:41.521243Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-08-27T09:29:42.547009Z, end-time: 2019-08-27T09:29:47.166075Z, 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-anndata/envs/latest/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/bin/python
Installing setuptools, pip, wheel...
done.

[rtd-command-info] start-time: 2019-08-27T09:29:47.247632Z, end-time: 2019-08-27T09:29:49.783171Z, duration: 2, exit-code: 0
python -m pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.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: 2019-08-27T09:29:49.860521Z, end-time: 2019-08-27T09:30:00.956730Z, duration: 11, exit-code: 0
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Building wheels for collected packages: mock, future, snowballstemmer
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Successfully built mock future snowballstemmer
Installing collected packages: Pygments, docutils, mock, pillow, alabaster, future, commonmark, sphinxcontrib-websupport, snowballstemmer, six, imagesize, attrs, pyparsing, packaging, MarkupSafe, Jinja2, certifi, urllib3, idna, chardet, requests, pytz, babel, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 attrs-19.1.0 babel-2.7.0 certifi-2019.6.16 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.17.1 idna-2.8 imagesize-1.1.0 mock-1.0.1 packaging-19.1 pillow-5.4.1 pyparsing-2.4.2 pytz-2019.2 readthedocs-sphinx-ext-1.0.0 recommonmark-0.5.0 requests-2.22.0 six-1.12.0 snowballstemmer-1.9.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.2 urllib3-1.25.3

[rtd-command-info] start-time: 2019-08-27T09:30:01.043624Z, end-time: 2019-08-27T09:30:14.841509Z, duration: 13, exit-code: 0
python -m pip install --exists-action=w --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.cache/pip -r docs/requires.txt
Requirement already satisfied: sphinx>=1.8 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from -r docs/requires.txt (line 2)) (1.8.5)
Collecting sphinx-autodoc-typehints (from -r docs/requires.txt (line 3))
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Collecting scanpydoc>=0.3.2 (from -r docs/requires.txt (line 4))
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Collecting pandas~=0.21 (from -r docs/requires.txt (line 6))
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Requirement already satisfied: requests>=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.22.0)
Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.1.0)
Requirement already satisfied: Pygments>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.3.1)
Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.1.2)
Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.7.0)
Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.9.0)
Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (0.7.12)
Requirement already satisfied: docutils>=0.11 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (0.14)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (41.0.1)
Requirement already satisfied: Jinja2>=2.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (2.10.1)
Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (19.1)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from sphinx>=1.8->-r docs/requires.txt (line 2)) (1.12.0)
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Requirement already satisfied: attrs in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages (from packaging->sphinx>=1.8->-r docs/requires.txt (line 2)) (19.1.0)
Collecting future-fstrings (from get_version->scanpydoc>=0.3.2->-r docs/requires.txt (line 4))
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ERROR: sphinx-autodoc-typehints 1.7.0 has requirement Sphinx>=2.1, but you'll have sphinx 1.8.5 which is incompatible.
Installing collected packages: sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, python-dateutil, numpy, pandas, scipy, h5py, natsort
Successfully installed future-fstrings-1.2.0 get-version-2.0.6 h5py-2.9.0 natsort-6.0.0 numpy-1.17.1 pandas-0.25.1 python-dateutil-2.8.0 scanpydoc-0.3.8 scipy-1.3.1 sphinx-autodoc-typehints-1.7.0

[rtd-command-info] start-time: 2019-08-27T09:30:15.578382Z, end-time: 2019-08-27T09:30:15.924330Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
import logging
from pathlib import Path
from datetime import datetime

HERE = Path(__file__).parent
sys.path.insert(0, str(HERE.parent))
import anndata  # noqa


logger = logging.getLogger(__name__)

for generated in HERE.glob('anndata.*.rst'):
    generated.unlink()


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


needs_sphinx = '1.7'  # autosummary bugfix

# General information
project = 'anndata'
author = anndata.__author__
copyright = f'{datetime.now():%Y}, {author}.'
version = anndata.__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
nitpicky = True  # Report broken links
suppress_warnings = ['ref.citation']


def setup(app):
    # Don’t allow broken links
    # app.warningiserror = True
    app.add_stylesheet('css/custom.css')


intersphinx_mapping = dict(
    h5py=('http://docs.h5py.org/en/latest/', None),
    loompy=('https://linnarssonlab.org/loompy/', 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),
    sklearn=('https://scikit-learn.org/stable/', None),
)


# -- 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='anndata',    # 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

def setup(app):
    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'),
]




###########################################################################
#          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/"),
    ("doc-builds", "/en/doc-builds/"),
    ],
    'downloads': [ 
    ("html", "//readthedocs.com/projects/icb-anndata/downloads/htmlzip/latest/"),
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-anndata',
    'name': u'anndata',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-anndata.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': 'anndata',
    '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': '926b82d9',
}




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: 2019-08-27T09:30:16.016941Z, end-time: 2019-08-27T09:30:17.340610Z, duration: 1, exit-code: 2
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.8.5

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py", line 93, in <module>
    from setuptools_scm import get_version
ModuleNotFoundError: No module named 'setuptools_scm'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/compat.py", line 6, in version
    from importlib.metadata import version
ModuleNotFoundError: No module named 'importlib.metadata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/conf.py", line 8, in <module>
    import anndata  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py", line 98, in <module>
    __version__ = version(__name__)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/compat.py", line 8, in version
    from importlib_metadata import version
ModuleNotFoundError: No module named 'importlib_metadata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/cmd/build.py", line 303, in build_main
    args.tags, args.verbosity, args.jobs, args.keep_going)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/application.py", line 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 203, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 380, in eval_config_file
    raise ConfigError(msg % traceback.format_exc())
sphinx.errors.ConfigError: There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py", line 93, in <module>
    from setuptools_scm import get_version
ModuleNotFoundError: No module named 'setuptools_scm'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/compat.py", line 6, in version
    from importlib.metadata import version
ModuleNotFoundError: No module named 'importlib.metadata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/conf.py", line 8, in <module>
    import anndata  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py", line 98, in <module>
    __version__ = version(__name__)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/compat.py", line 8, in version
    from importlib_metadata import version
ModuleNotFoundError: No module named 'importlib_metadata'


Configuration error:
There is a programmable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py", line 93, in <module>
    from setuptools_scm import get_version
ModuleNotFoundError: No module named 'setuptools_scm'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/compat.py", line 6, in version
    from importlib.metadata import version
ModuleNotFoundError: No module named 'importlib.metadata'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 368, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/docs/conf.py", line 8, in <module>
    import anndata  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/__init__.py", line 98, in <module>
    __version__ = version(__name__)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/latest/anndata/compat.py", line 8, in version
    from importlib_metadata import version
ModuleNotFoundError: No module named 'importlib_metadata'