Read the Docs build information
Build id: 208415
Project: icb-scanpy
Version: latest
Commit: 18933d0296a256279baa72522343c3ed9535421d
Date: 2019-05-15T07:40:34.877713Z
State: finished
Success: False


[rtd-command-info] start-time: 2019-05-15T07:40:35.432219Z, end-time: 2019-05-15T07:40:37.586514Z, 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: 2019-05-15T07:40:37.811411Z, end-time: 2019-05-15T07:40:37.907277Z, 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 18933d0 added umap to docs requirements

[rtd-command-info] start-time: 2019-05-15T07:40:37.966671Z, end-time: 2019-05-15T07:40:37.976463Z, duration: 0, exit-code: 0
git clean -d -f -f


[rtd-command-info] start-time: 2019-05-15T07:40:38.620776Z, end-time: 2019-05-15T07:40:41.851127Z, duration: 3, exit-code: 0
python3.6 -mvirtualenv --no-site-packages --no-download 
Using base prefix '/home/docs/.pyenv/versions/3.6.4'
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: 2019-05-15T07:40:41.913050Z, end-time: 2019-05-15T07:40:44.316826Z, 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
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Installing collected packages: pip
  Found existing installation: pip 18.1
    Uninstalling pip-18.1:
      Successfully uninstalled pip-18.1
Successfully installed pip-19.1.1

[rtd-command-info] start-time: 2019-05-15T07:40:44.374499Z, end-time: 2019-05-15T07:40:55.198113Z, duration: 10, exit-code: 0
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Successfully built mock future
Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, six, pyparsing, packaging, MarkupSafe, Jinja2, snowballstemmer, pytz, babel, imagesize, urllib3, certifi, chardet, idna, requests, sphinxcontrib-websupport, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext
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    Uninstalling setuptools-40.6.3:
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Successfully installed Jinja2-2.10.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.6.0 certifi-2019.3.9 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-19.0 pillow-5.4.1 pyparsing-2.4.0 pytz-2019.1 readthedocs-sphinx-ext-0.5.17 recommonmark-0.5.0 requests-2.21.0 setuptools-40.9.0 six-1.12.0 snowballstemmer-1.2.1 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.1.0 urllib3-1.24.3

[rtd-command-info] start-time: 2019-05-15T07:40:55.290784Z, end-time: 2019-05-15T07:41:27.014259Z, duration: 31, 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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  Downloading https://files.pythonhosted.org/packages/ce/47/daed787cca0a5a905fdb239c6f893b5e5bd520d07a665809d09cd9cc8160/future_fstrings-1.1.0-py2.py3-none-any.whl
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  Downloading https://files.pythonhosted.org/packages/2d/27/610ef458455cb1bcc4b454cebab43de3579e43d080af872727b9ac3146c8/get_version-2.0.6-py3-none-any.whl (43kB)
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  Downloading https://files.pythonhosted.org/packages/c1/e2/4db8df8f6cddc98e7d7c537245ef2f4e41a1ed17bf0c3177ab3cc6beac7f/numpy-1.16.3-cp36-cp36m-manylinux1_x86_64.whl (17.3MB)
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Collecting python-dateutil>=2.1 (from matplotlib>=2.2->-r docs/requirements.txt (line 10))
  Downloading https://files.pythonhosted.org/packages/41/17/c62faccbfbd163c7f57f3844689e3a78bae1f403648a6afb1d0866d87fbb/python_dateutil-2.8.0-py2.py3-none-any.whl (226kB)
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Collecting mock>=2.0 (from tables->-r docs/requirements.txt (line 15))
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Building wheels for collected packages: anndata, networkx, umap
  Building wheel for anndata (setup.py): started
  Building wheel for anndata (setup.py): finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/7f/e5/74/a94b1e21a75fbdff29343aeb9970279fbc9ab8a2a8cfaa87dc
  Building wheel for networkx (setup.py): started
  Building wheel for networkx (setup.py): finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/de/63/64/3699be2a9d0ccdb37c7f16329acf3863fd76eda58c39c737af
  Building wheel for umap (setup.py): started
  Building wheel for umap (setup.py): finished with status 'done'
  Stored in directory: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/.cache/pip/wheels/7b/29/33/b4d917dc95f69c0a060e2ab012d95e15db9ed4cc0b94ccac26
Successfully built anndata networkx umap
Installing collected packages: sphinxcontrib-devhelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-applehelp, sphinx, sphinx-autodoc-typehints, future-fstrings, get-version, scanpydoc, numpy, python-dateutil, pandas, scipy, h5py, natsort, anndata, cycler, kiwisolver, matplotlib, seaborn, mock, numexpr, tables, joblib, scikit-learn, decorator, networkx, llvmlite, numba, tqdm, umap
  Found existing installation: Sphinx 1.8.5
    Uninstalling Sphinx-1.8.5:
      Successfully uninstalled Sphinx-1.8.5
  Found existing installation: mock 1.0.1
    Uninstalling mock-1.0.1:
      Successfully uninstalled mock-1.0.1
Successfully installed anndata-0.6.19 cycler-0.10.0 decorator-4.4.0 future-fstrings-1.1.0 get-version-2.0.6 h5py-2.9.0 joblib-0.13.2 kiwisolver-1.1.0 llvmlite-0.28.0 matplotlib-3.0.3 mock-3.0.5 natsort-6.0.0 networkx-2.3 numba-0.43.1 numexpr-2.6.9 numpy-1.16.3 pandas-0.24.2 python-dateutil-2.8.0 scanpydoc-0.3.3 scikit-learn-0.21.0 scipy-1.2.1 seaborn-0.9.0 sphinx-2.0.1 sphinx-autodoc-typehints-1.6.0 sphinxcontrib-applehelp-1.0.1 sphinxcontrib-devhelp-1.0.1 sphinxcontrib-htmlhelp-1.0.2 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.2 sphinxcontrib-serializinghtml-1.1.3 tables-3.5.1 tqdm-4.32.1 umap-0.1.1

[rtd-command-info] start-time: 2019-05-15T07:41:27.545699Z, end-time: 2019-05-15T07:41:27.605719Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
from pathlib import Path
from datetime import datetime

import matplotlib  # noqa
# Don’t use tkinter agg when importing scanpy → … → matplotlib
matplotlib.use('agg')

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


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


needs_sphinx = '1.7'  # autosummary bugfix

# General information
project = 'Scanpy'
author = scanpy.__author__
copyright = f'{datetime.now():%Y}, {author}.'
version = scanpy.__version__.replace('.dirty', '')
release = version

# default settings
templates_path = ['_templates']
source_suffix = '.rst'
master_doc = 'index'
default_role = 'literal'
exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
pygments_style = 'sphinx'

extensions = [
    'sphinx.ext.autodoc',
    'sphinx.ext.intersphinx',
    'sphinx.ext.doctest',
    'sphinx.ext.coverage',
    'sphinx.ext.mathjax',
    'sphinx.ext.napoleon',
    'sphinx.ext.autosummary',
    # 'plot_generator',
    # 'plot_directive',
    'sphinx_autodoc_typehints',  # needs to be after napoleon
    # 'ipython_directive',
    # 'ipython_console_highlighting',
    'scanpydoc',
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = 'bysource'
# autodoc_default_flags = ['members']
napoleon_google_docstring = False
napoleon_numpy_docstring = True
napoleon_include_init_with_doc = False
napoleon_use_rtype = True  # having a separate entry generally helps readability
napoleon_use_param = True
napoleon_custom_sections = [('Params', 'Parameters')]
todo_include_todos = False

intersphinx_mapping = dict(
    anndata=('https://anndata.readthedocs.io/en/latest/', None),
    bbknn=('https://bbknn.readthedocs.io/en/latest/', None),
    leidenalg=('https://leidenalg.readthedocs.io/en/latest/', None),
    louvain=('https://louvain-igraph.readthedocs.io/en/latest/', None),
    matplotlib=('https://matplotlib.org/', None),
    networkx=('https://networkx.github.io/documentation/networkx-1.10/', None),
    numpy=('https://docs.scipy.org/doc/numpy/', None),
    pandas=('http://pandas.pydata.org/pandas-docs/stable/', None),
    python=('https://docs.python.org/3', None),
    scipy=('https://docs.scipy.org/doc/scipy/reference/', None),
    sklearn=('https://scikit-learn.org/stable/', None),
    scanpy_tutorials=('https://scanpy-tutorials.readthedocs.io/en/latest', None),
)


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


html_theme = 'sphinx_rtd_theme'
html_theme_options = dict(
    navigation_depth=4,
    logo_only=True,           # Only show the logo
)
html_context = dict(
    display_github=True,      # Integrate GitHub
    github_user='theislab',   # Username
    github_repo='scanpy',     # Repo name
    github_version='master',  # Version
    conf_py_path='/docs/',    # Path in the checkout to the docs root
)
html_static_path = ['_static']
html_logo = '_static/img/Scanpy_Logo_RGB.png'
gh_url = 'https://github.com/{github_user}/{github_repo}'.format_map(html_context)


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


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


htmlhelp_basename = f'{project}doc'
doc_title = f'{project} Documentation'
latex_documents = [
    (master_doc, f'{project}.tex', doc_title, author, 'manual'),
]
man_pages = [
    (master_doc, project, doc_title, [author], 1)
]
texinfo_documents = [
    (master_doc, project, doc_title, author, project, 'One line description of project.', 'Miscellaneous'),
]


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


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


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


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


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


import re
from sphinx.ext.napoleon import NumpyDocstring


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


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


NumpyDocstring._parse_returns_section = scanpy_parse_returns_section


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


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




###########################################################################
#          auto-created readthedocs.org specific configuration            #
###########################################################################


#
# The following code was added during an automated build on readthedocs.org
# It is auto created and injected for every build. The result is based on the
# conf.py.tmpl file found in the readthedocs.org codebase:
# https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#


import importlib
import sys
import os.path
from six import string_types

from sphinx import version_info

# Get suffix for proper linking to GitHub
# This is deprecated in Sphinx 1.3+,
# as each page can have its own suffix
if globals().get('source_suffix', False):
    if isinstance(source_suffix, string_types):
        SUFFIX = source_suffix
    elif isinstance(source_suffix, (list, tuple)):
        # Sphinx >= 1.3 supports list/tuple to define multiple suffixes
        SUFFIX = source_suffix[0]
    elif isinstance(source_suffix, dict):
        # Sphinx >= 1.8 supports a mapping dictionary for mulitple 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/"),
    ],
    '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': '18933d02',
}




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: 2019-05-15T07:41:27.675552Z, end-time: 2019-05-15T07:41:28.762814Z, duration: 1, exit-code: 2
python sphinx-build -T -E -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html
Running Sphinx v2.0.1

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 361, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 86, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 11, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 27, in <module>
    check_versions()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/utils.py", line 43, in check_versions
    if umap.__version__ < LooseVersion('0.3.0'):
AttributeError: module 'umap' has no attribute '__version__'

During handling of the above exception, another exception occurred:

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 283, 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 201, in __init__
    self.config = Config.read(self.confdir, confoverrides or {}, self.tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 196, in read
    namespace = eval_config_file(filename, tags)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 371, 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-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 361, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 86, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 11, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 27, in <module>
    check_versions()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/utils.py", line 43, in check_versions
    if umap.__version__ < LooseVersion('0.3.0'):
AttributeError: module 'umap' has no attribute '__version__'


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-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/config.py", line 361, in eval_config_file
    execfile_(filename, namespace)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.6/site-packages/sphinx/util/pycompat.py", line 86, in execfile_
    exec(code, _globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/conf.py", line 11, in <module>
    import scanpy  # noqa
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/__init__.py", line 27, in <module>
    check_versions()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/scanpy/utils.py", line 43, in check_versions
    if umap.__version__ < LooseVersion('0.3.0'):
AttributeError: module 'umap' has no attribute '__version__'