Read the Docs build information
Build id: 140058
Project: icb-anndata
Version: stable
Commit: db905235cfb2d2335ef76df2eba18bfd420c0794
Date: 2018-09-05T14:38:35.656061Z
State: finished
Success: False


[rtd-command-info] start-time: 2018-09-05T19:39:07.321471Z, end-time: 2018-09-05T19:39:07.688909Z, duration: 0, exit-code: 0
git clone --recursive https://github.com/theislab/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2018-09-05T19:39:07.747780Z, end-time: 2018-09-05T19:39:07.763495Z, duration: 0, exit-code: 0
git checkout --force db905235cfb2d2335ef76df2eba18bfd420c0794
Note: checking out 'db905235cfb2d2335ef76df2eba18bfd420c0794'.

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 db90523... update write_loom to write layers (#53)

[rtd-command-info] start-time: 2018-09-05T19:39:07.823515Z, end-time: 2018-09-05T19:39:07.834724Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2018-09-05T19:39:07.951361Z, end-time: 2018-09-05T19:39:07.961478Z, duration: 0, exit-code: 0
git branch -r
origin/2d
  origin/HEAD -> origin/master
  origin/backed
  origin/logging
  origin/master

[rtd-command-info] start-time: 2018-09-05T19:39:08.592916Z, end-time: 2018-09-05T19:39:11.374915Z, 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-anndata/envs/stable/bin/python3.6
Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/bin/python
Installing setuptools, pip, wheel...done.

[rtd-command-info] start-time: 2018-09-05T19:39:11.434713Z, end-time: 2018-09-05T19:39:19.079175Z, duration: 7, exit-code: 0
python pip install --upgrade --cache-dir /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/.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
Collecting Pygments==2.2.0
  Using cached https://files.pythonhosted.org/packages/02/ee/b6e02dc6529e82b75bb06823ff7d005b141037cb1416b10c6f00fc419dca/Pygments-2.2.0-py2.py3-none-any.whl
Collecting setuptools<40
  Using cached https://files.pythonhosted.org/packages/7f/e1/820d941153923aac1d49d7fc37e17b6e73bfbd2904959fffbad77900cf92/setuptools-39.2.0-py2.py3-none-any.whl
Collecting docutils==0.13.1
  Using cached https://files.pythonhosted.org/packages/7c/30/8fb30d820c012a6f701a66618ce065b6d61d08ac0a77e47fc7808dbaee47/docutils-0.13.1-py3-none-any.whl
Collecting mock==1.0.1
Collecting pillow==2.6.1
Collecting alabaster!=0.7.5,<0.8,>=0.7
  Using cached https://files.pythonhosted.org/packages/6e/71/c3648cc2f675063dbe2d669004a59e4a5120172713a1de3c3b14144d4b31/alabaster-0.7.11-py2.py3-none-any.whl
Collecting commonmark==0.5.4
Collecting recommonmark==0.4.0
  Using cached https://files.pythonhosted.org/packages/df/a5/8ee4b84af7f997dfdba71254a88008cfc19c49df98983c9a4919e798f8ce/recommonmark-0.4.0-py2.py3-none-any.whl
Collecting sphinx<1.8
  Using cached https://files.pythonhosted.org/packages/90/f9/a0babe32c78480994e4f1b93315558f5ed756104054a7029c672a8d77b72/Sphinx-1.7.9-py2.py3-none-any.whl
Collecting sphinx-rtd-theme<0.5
  Using cached https://files.pythonhosted.org/packages/87/30/7460f7b77b6e8a080dd3688f750fe5d5666c49358f8941449c5b128fa97d/sphinx_rtd_theme-0.4.1-py2.py3-none-any.whl
Collecting readthedocs-sphinx-ext<0.6
  Using cached https://files.pythonhosted.org/packages/54/7a/26d18b225af6041f99457c002d3f27485732864ac984d3c4c56f27d73ef1/readthedocs_sphinx_ext-0.5.14-py2.py3-none-any.whl
Collecting packaging (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/ad/c2/b500ea05d5f9f361a562f089fc91f77ed3b4783e13a08a3daf82069b1224/packaging-17.1-py2.py3-none-any.whl
Collecting babel!=2.0,>=1.3 (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/b8/ad/c6f60602d3ee3d92fbed87675b6fb6a6f9a38c223343ababdb44ba201f10/Babel-2.6.0-py2.py3-none-any.whl
Collecting sphinxcontrib-websupport (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/52/69/3c2fbdc3702358c5b34ee25e387b24838597ef099761fc9a42c166796e8f/sphinxcontrib_websupport-1.1.0-py2.py3-none-any.whl
Collecting imagesize (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/fc/b6/aef66b4c52a6ad6ac18cf6ebc5731ed06d8c9ae4d3b2d9951f261150be67/imagesize-1.1.0-py2.py3-none-any.whl
Collecting Jinja2>=2.3 (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/7f/ff/ae64bacdfc95f27a016a7bed8e8686763ba4d277a78ca76f32659220a731/Jinja2-2.10-py2.py3-none-any.whl
Collecting six>=1.5 (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/67/4b/141a581104b1f6397bfa78ac9d43d8ad29a7ca43ea90a2d863fe3056e86a/six-1.11.0-py2.py3-none-any.whl
Collecting snowballstemmer>=1.1 (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/d4/6c/8a935e2c7b54a37714656d753e4187ee0631988184ed50c0cf6476858566/snowballstemmer-1.2.1-py2.py3-none-any.whl
Collecting requests>=2.0.0 (from sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/65/47/7e02164a2a3db50ed6d8a6ab1d6d60b69c4c3fdf57a284257925dfc12bda/requests-2.19.1-py2.py3-none-any.whl
Collecting pyparsing>=2.0.2 (from packaging->sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/6a/8a/718fd7d3458f9fab8e67186b00abdd345b639976bc7fb3ae722e1b026a50/pyparsing-2.2.0-py2.py3-none-any.whl
Collecting pytz>=0a (from babel!=2.0,>=1.3->sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/30/4e/27c34b62430286c6d59177a0842ed90dc789ce5d1ed740887653b898779a/pytz-2018.5-py2.py3-none-any.whl
Collecting MarkupSafe>=0.23 (from Jinja2>=2.3->sphinx<1.8)
Collecting idna<2.8,>=2.5 (from requests>=2.0.0->sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/4b/2a/0276479a4b3caeb8a8c1af2f8e4355746a97fab05a372e4a2c6a6b876165/idna-2.7-py2.py3-none-any.whl
Collecting chardet<3.1.0,>=3.0.2 (from requests>=2.0.0->sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/bc/a9/01ffebfb562e4274b6487b4bb1ddec7ca55ec7510b22e4c51f14098443b8/chardet-3.0.4-py2.py3-none-any.whl
Collecting certifi>=2017.4.17 (from requests>=2.0.0->sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/df/f7/04fee6ac349e915b82171f8e23cee63644d83663b34c539f7a09aed18f9e/certifi-2018.8.24-py2.py3-none-any.whl
Collecting urllib3<1.24,>=1.21.1 (from requests>=2.0.0->sphinx<1.8)
  Using cached https://files.pythonhosted.org/packages/bd/c9/6fdd990019071a4a32a5e7cb78a1d92c53851ef4f56f62a3486e6a7d8ffb/urllib3-1.23-py2.py3-none-any.whl
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, commonmark, recommonmark, six, pyparsing, packaging, pytz, babel, sphinxcontrib-websupport, imagesize, MarkupSafe, Jinja2, snowballstemmer, idna, chardet, certifi, urllib3, requests, 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-1.0 Pygments-2.2.0 alabaster-0.7.11 babel-2.6.0 certifi-2018.8.24 chardet-3.0.4 commonmark-0.5.4 docutils-0.13.1 idna-2.7 imagesize-1.1.0 mock-1.0.1 packaging-17.1 pillow-2.6.1 pyparsing-2.2.0 pytz-2018.5 readthedocs-sphinx-ext-0.5.14 recommonmark-0.4.0 requests-2.19.1 setuptools-39.2.0 six-1.11.0 snowballstemmer-1.2.1 sphinx-1.7.9 sphinx-rtd-theme-0.4.1 sphinxcontrib-websupport-1.1.0 urllib3-1.23
You are using pip version 9.0.3, however version 18.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

[rtd-command-info] start-time: 2018-09-05T19:39:19.521524Z, end-time: 2018-09-05T19:39:19.595699Z, duration: 0, exit-code: 0
cat docs/conf.py
import os
import sys
import time
import inspect
from pathlib import Path, PurePosixPath
import logging

HERE = Path(__file__).parent
sys.path.insert(0, str(HERE / '..'))

import anndata


logger = logging.getLogger(__name__)

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


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

# If your documentation needs a minimal Sphinx version, state it here.
#
# needs_sphinx = '1.0'

# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
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',
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_mock_imports = ['_tkinter']  # why this?
autodoc_member_order = 'bysource'
#autodoc_default_flags = ['members']
napoleon_use_param = True

intersphinx_mapping = dict(
    python=('https://docs.python.org/3', None),
    h5py=('http://docs.h5py.org/en/latest/', None)
)

templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
project = 'anndata'
copyright = '{}, Alex Wolf, Philipp Angerer, Sergei Rybakov'.format(time.strftime("%Y"))
author = 'Alex Wolf, Philipp Angerer, Sergei Rybakov'

version = anndata.__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 = {
    'navigation_depth': 2,
}
html_context = {
    '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
    'css_files': [               # Additional CSS
        '_static/css/override.css',
    ],
}
if 'READTHEDOCS' in os.environ:
    # For some reason, RTD doesn’t insert their stuff anymore once we add custom CSS files.
    html_context['css_files'].insert(0, 'https://media.readthedocs.org/css/sphinx_rtd_theme.css')

html_static_path = ['_static']

# -- Options for HTMLHelp output ------------------------------------------

# Output file base name for HTML help builder.
htmlhelp_basename = 'anndatadoc'


# -- Options for LaTeX output ---------------------------------------------

latex_elements = {
    # The paper size ('letterpaper' or 'a4paper').
    #
    # 'papersize': 'letterpaper',

    # The font size ('10pt', '11pt' or '12pt').
    #
    # 'pointsize': '10pt',

    # Additional stuff for the LaTeX preamble.
    #
    # 'preamble': '',

    # Latex figure (float) alignment
    #
    # 'figure_align': 'htbp',
}

# Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title,
#  author, documentclass [howto, manual, or own class]).
latex_documents = [
    (master_doc, 'anndata.tex', 'anndata Documentation',
     'Alex Wolf, Philipp Angerer', 'manual'),
]


# -- Options for manual page output ---------------------------------------

# One entry per manual page. List of tuples
# (source start file, name, description, authors, manual section).
man_pages = [
    (master_doc, 'anndata', 'anndata Documentation',
     [author], 1)
]


# -- Options for Texinfo output -------------------------------------------

# Grouping the document tree into Texinfo files. List of tuples
# (source start file, target name, title, author,
#  dir menu entry, description, category)
texinfo_documents = [
    (master_doc, 'anndata', 'anndata Documentation',
     author, 'anndata', 'One line description of project.',
     'Miscellaneous'),
]


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


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):
    """Get the full GitHub URL for some object’s qualname."""
    obj, module = get_obj_module(qualname)
    github_url = github_url1
    try:
        path = PurePosixPath(Path(module.__file__).resolve().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 = '#L{}-L{}'.format(start, end) if start and end else ''
    return '{}/{}{}'.format(github_url, path, fragment)


# 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['modurl'] = modurl


# -- 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):
                    typename = ''.join(n.astext() for n in fieldtype)
                    head += makerefs(self.typerolename, typename, 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 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 = False
if 'html_theme' in globals():
    if html_theme in ['default']:
        # Allow people to bail with a hack of having an html_style
        if not 'html_style' in globals():
            import sphinx_rtd_theme
            html_theme = 'sphinx_rtd_theme'
            html_style = None
            html_theme_options = {}
            if 'html_theme_path' in globals():
                html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
            else:
                html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]

            using_rtd_theme = True
else:
    import sphinx_rtd_theme
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}
    if 'html_theme_path' in globals():
        html_theme_path.append(sphinx_rtd_theme.get_html_theme_path())
    else:
        html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
    using_rtd_theme = True

if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    if 'http' not in settings.MEDIA_URL:
        websupport2_static_url = 'https://media.readthedocs.com/'
    else:
        websupport2_static_url = 'https://media.readthedocs.com/media//static'


#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/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-anndata',
    'name': u'anndata',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://icb-anndata.readthedocs-hosted.com/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'theislab',
    'github_repo': 'anndata',
    'github_version': 'db905235cfb2d2335ef76df2eba18bfd420c0794',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'db905235cfb2d2335ef76df2eba18bfd420c0794',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'db905235cfb2d2335ef76df2eba18bfd420c0794',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    
    'commit': 'db905235',
    
}




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"]

# Build the json artifacts with the html build step
rtd_generate_json_artifacts = True

[rtd-command-info] start-time: 2018-09-05T19:39:19.658671Z, end-time: 2018-09-05T19:39:20.148666Z, duration: 0, exit-code: 2
python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v1.7.9

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/config.py", line 161, in __init__
    execfile_(filename, config)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "conf.py", line 11, in <module>
    import anndata
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/../anndata/__init__.py", line 1, in <module>
    from .base import AnnData, _MAIN_NARRATIVE
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/../anndata/base.py", line 13, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'

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/stable/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-anndata/envs/stable/lib/python3.6/site-packages/sphinx/application.py", line 163, in __init__
    confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/config.py", line 167, in __init__
    raise ConfigError(CONFIG_ERROR % traceback.format_exc())
sphinx.errors.ConfigError: There is a programable error in your configuration file:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/config.py", line 161, in __init__
    execfile_(filename, config)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "conf.py", line 11, in <module>
    import anndata
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/../anndata/__init__.py", line 1, in <module>
    from .base import AnnData, _MAIN_NARRATIVE
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/../anndata/base.py", line 13, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'


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

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/config.py", line 161, in __init__
    execfile_(filename, config)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/stable/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 150, in execfile_
    exec_(code, _globals)
  File "conf.py", line 11, in <module>
    import anndata
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/../anndata/__init__.py", line 1, in <module>
    from .base import AnnData, _MAIN_NARRATIVE
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/stable/docs/../anndata/base.py", line 13, in <module>
    import numpy as np
ModuleNotFoundError: No module named 'numpy'