Read the Docs build information
Build id: 1461741
Project: icb-anndata
Version: 947
Commit: d856f9b9da34975d2f60eea852051fc14b6c35db
Date: 2023-05-09T13:39:14.396790Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2023-05-09T13:39:16.313788Z, end-time: 2023-05-09T13:39:17.555268Z, duration: 1, exit-code: 0
git clone --no-single-branch --depth 50 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2023-05-09T13:39:17.767853Z, end-time: 2023-05-09T13:39:18.345171Z, duration: 0, exit-code: 0
git fetch origin --force --tags --prune --prune-tags --depth 50 pull/947/head:external-947
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/947/head -> external-947

[rtd-command-info] start-time: 2023-05-09T13:39:18.531532Z, end-time: 2023-05-09T13:39:18.613920Z, duration: 0, exit-code: 0
git checkout --force d856f9b9da34975d2f60eea852051fc14b6c35db
Note: switching to 'd856f9b9da34975d2f60eea852051fc14b6c35db'.

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 switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at d856f9b (fix): add columns attr + cleanup

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git clean -d -f -f


[rtd-command-info] start-time: 2023-05-09T13:39:19.169113Z, end-time: 2023-05-09T13:39:19.268898Z, duration: 0, exit-code: 0
git submodule sync


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git submodule update --init --force --recursive docs/tutorials/notebooks
Submodule 'docs/tutorials/notebooks' (https://github.com/scverse/anndata-tutorials) registered for path 'docs/tutorials/notebooks'
Cloning into '/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2023-05-09T13:39:25.478967Z, end-time: 2023-05-09T13:39:25.564416Z, duration: 0, exit-code: 0
asdf global python 3.10.8


[rtd-command-info] start-time: 2023-05-09T13:39:26.096077Z, end-time: 2023-05-09T13:39:26.932234Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.10.8.final.0-64 in 510ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, setuptools=bundle, wheel=bundle, via=copy, app_data_dir=/home/docs/.local/share/virtualenv)
    added seed packages: pip==21.2.3, setuptools==57.4.0, wheel==0.37.0
  activators BashActivator,CShellActivator,FishActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2023-05-09T13:39:27.137752Z, end-time: 2023-05-09T13:39:39.458546Z, duration: 12, exit-code: 0
python -m pip install --upgrade --no-cache-dir pip setuptools
Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/947/lib/python3.10/site-packages (21.2.3)
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Installing collected packages: setuptools, pip
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    Uninstalling setuptools-57.4.0:
      Successfully uninstalled setuptools-57.4.0
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    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
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Successfully installed pip-23.1.2 setuptools-67.7.2

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python -m pip install --upgrade --no-cache-dir pillow mock==1.0.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.9.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.3 jinja2<3.1.0
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Building wheels for collected packages: mock
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Successfully built mock
Installing collected packages: snowballstemmer, mock, commonmark, urllib3, sphinxcontrib-serializinghtml, six, Pygments, pillow, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, sphinxcontrib-websupport, requests, jinja2, sphinx, readthedocs-sphinx-ext, sphinx-rtd-theme, recommonmark
Successfully installed MarkupSafe-2.1.2 Pygments-2.15.1 alabaster-0.7.13 babel-2.12.1 certifi-2023.5.7 charset-normalizer-3.1.0 commonmark-0.9.1 docutils-0.17.1 idna-3.4 imagesize-1.4.1 jinja2-3.0.3 mock-1.0.1 packaging-23.1 pillow-9.5.0 readthedocs-sphinx-ext-2.2.0 recommonmark-0.5.0 requests-2.30.0 six-1.16.0 snowballstemmer-2.2.0 sphinx-1.8.6 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-2.0.2

[rtd-command-info] start-time: 2023-05-09T13:39:51.905892Z, end-time: 2023-05-09T13:40:42.956274Z, duration: 51, exit-code: 0
python -m pip install --upgrade --upgrade-strategy eager --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/947
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Building wheels for collected packages: anndata, asciitree
  Building wheel for anndata (pyproject.toml): started
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  Created wheel for anndata: filename=anndata-0.9.0rc2.dev117+gd856f9b-py3-none-any.whl size=456232 sha256=2989b8e46d552240e3e78833822ac25dd8ac4230202d91c49648c50542664281
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      Successfully uninstalled Jinja2-3.0.3
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  Attempting uninstall: sphinx
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    Uninstalling Sphinx-1.8.6:
      Successfully uninstalled Sphinx-1.8.6
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Successfully installed IPython-8.13.2 Jinja2-3.1.2 anndata-0.9.0rc2.dev117+gd856f9b asciitree-0.3.3 asttokens-2.2.1 attrs-23.1.0 awkward-2.1.4 awkward-cpp-15 backcall-0.2.0 beautifulsoup4-4.12.2 bleach-6.0.0 contourpy-1.0.7 cycler-0.11.0 decorator-5.1.1 defusedxml-0.7.1 docutils-0.18.1 dunamai-1.16.0 entrypoints-0.4 executing-1.2.0 fasteners-0.18 fastjsonschema-2.16.3 fonttools-4.39.3 get_version-3.5.4 h5py-3.8.0 jedi-0.18.2 jsonschema-4.17.3 jupyter-client-8.2.0 jupyter-core-5.3.0 jupyterlab-pygments-0.2.2 kiwisolver-1.4.4 markdown-it-py-2.2.0 matplotlib-3.7.1 matplotlib-inline-0.1.6 mdit-py-plugins-0.3.5 mdurl-0.1.2 mistune-2.0.5 myst_parser-1.0.0 natsort-8.3.1 nbclient-0.7.4 nbconvert-7.4.0 nbformat-5.8.0 nbsphinx-0.9.1 numcodecs-0.11.0 numpy-1.24.3 pandas-2.0.1 pandocfilters-1.5.0 parso-0.8.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-3.5.0 prompt-toolkit-3.0.38 ptyprocess-0.7.0 pure-eval-0.2.2 pyparsing-3.0.9 pyrsistent-0.19.3 python-dateutil-2.8.2 pytz-2023.3 pyyaml-6.0 pyzmq-25.0.2 scanpydoc-0.7.8 scipy-1.10.1 soupsieve-2.4.1 sphinx-6.2.1 sphinx-autodoc-typehints-1.23.0 sphinx-rtd-theme-1.2.0 sphinx_issues-3.0.1 sphinxcontrib-applehelp-1.0.4 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.1 sphinxcontrib-jquery-4.1 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxext.opengraph-0.8.2 stack-data-0.6.2 tinycss2-1.2.1 tornado-6.3.1 traitlets-5.9.0 typing-extensions-4.5.0 tzdata-2023.3 wcwidth-0.2.6 webencodings-0.5.1 zarr-2.14.2

[rtd-command-info] start-time: 2023-05-09T13:40:44.673370Z, end-time: 2023-05-09T13:40:44.737557Z, duration: 0, exit-code: 0
cat docs/conf.py
import sys
import logging
from pathlib import Path
from datetime import datetime

from sphinx.application import Sphinx

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
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 = f"{project} developers"
copyright = f"{datetime.now():%Y}, {author}"
version = anndata.__version__.replace(".dirty", "")
release = version

# default settings
templates_path = ["_templates"]
html_static_path = ["_static"]
source_suffix = [".rst", ".md"]
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/notebooks/*.rst",
]
pygments_style = "sphinx"

extensions = [
    "myst_parser",
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.doctest",
    "sphinx.ext.coverage",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx.ext.autosummary",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "sphinx_issues",
    "sphinxext.opengraph",
    "scanpydoc",
    "nbsphinx",
    "IPython.sphinxext.ipython_console_highlighting",
]
myst_enable_extensions = [
    "html_image",  # So README.md can be used on github and sphinx docs
]

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
issues_github_path = "scverse/anndata"
# 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")]
typehints_defaults = "braces"
todo_include_todos = False
nitpicky = True  # Report broken links
nitpick_ignore = [
    ("py:class", "scipy.sparse.base.spmatrix"),
    ("py:meth", "pandas.DataFrame.iloc"),
    ("py:meth", "pandas.DataFrame.loc"),
    ("py:class", "anndata._core.views.ArrayView"),
    ("py:class", "anndata._core.raw.Raw"),
    *[
        ("py:class", f"anndata._core.aligned_mapping.{cls}{kind}")
        for cls in "Layers AxisArrays PairwiseArrays".split()
        for kind in ["", "View"]
    ],
]
suppress_warnings = [
    "ref.citation",
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
]


def setup(app: Sphinx):
    # Don’t allow broken links. DO NOT CHANGE THIS LINE, fix problems instead.
    app.warningiserror = False


intersphinx_mapping = dict(
    h5py=("https://docs.h5py.org/en/latest/", None),
    hdf5plugin=("https://hdf5plugin.readthedocs.io/en/latest/", None),
    loompy=("https://linnarssonlab.org/loompy/", None),
    numpy=("https://numpy.org/doc/stable/", None),
    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
    python=("https://docs.python.org/3", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
    zarr=("https://zarr.readthedocs.io/en/stable/", None),
    xarray=("https://xarray.pydata.org/en/stable/", None),
)
qualname_overrides = {
    "h5py._hl.group.Group": "h5py.Group",
    "h5py._hl.files.File": "h5py.File",
    "h5py._hl.dataset.Dataset": "h5py.Dataset",
    "anndata._core.anndata.AnnData": "anndata.AnnData",
}

# -- Social cards ---------------------------------------------------------

ogp_site_url = "https://anndata.readthedocs.io/"
ogp_image = "https://anndata.readthedocs.io/en/latest/_static/img/anndata_schema.svg"

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


html_theme = "scanpydoc"
html_theme_options = dict(navigation_depth=4)
html_context = dict(
    display_github=True,  # Integrate GitHub
    github_user="scverse",  # Username
    github_repo="anndata",  # Repo name
    github_version="main",  # Version
    conf_py_path="/docs/",  # Path in the checkout to the docs root
)
issues_github_path = "{github_user}/{github_repo}".format_map(html_context)
html_show_sphinx = False


# -- 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/main/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl
#
# Note: this file shouldn't rely on extra dependencies.

import importlib
import sys
import os.path

# Borrowed from six.
PY3 = sys.version_info[0] == 3
string_types = str if PY3 else basestring

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:
    html_theme = 'sphinx_rtd_theme'
    html_style = None
    html_theme_options = {}


# This following legacy behavior will gradually be sliced out until its deprecated and removed.
# Skipped for Sphinx 6+
# Skipped by internal Feature flag SKIP_SPHINX_HTML_THEME_PATH
# Skipped by all new projects since SKIP_SPHINX_HTML_THEME_PATH's introduction (jan 2023)
if (
        using_rtd_theme
        and version_info < (6,0)
        and not False
    ):
    theme = importlib.import_module('sphinx_rtd_theme')
    if 'html_theme_path' in globals():
        html_theme_path.append(theme.get_html_theme_path())
    else:
        html_theme_path = [theme.get_html_theme_path()]

# Define websupport2_base_url and websupport2_static_url
if globals().get('websupport2_base_url', False):
    websupport2_base_url = 'https://readthedocs.com/websupport'
    websupport2_static_url = 'https://assets.readthedocs.com/'


#Add project information to the template context.
context = {
    'using_theme': using_rtd_theme,
    'html_theme': html_theme,
    'current_version': "947",
    'version_slug': "947",
    'MEDIA_URL': "https://media.readthedocs.com/media/",
    'STATIC_URL': "https://assets.readthedocs.com/",
    'PRODUCTION_DOMAIN': "readthedocs.com",
    'proxied_static_path': "/_/static/",
    'versions': [
    ("latest", "/en/latest/"),
    ("stable", "/en/stable/"),
    ("0.7.8", "/en/0.7.8/"),
    ("0.4.1", "/en/0.4.1/"),
    ("0.3", "/en/0.3/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-anndata',
    'name': u'anndata',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': 'https://anndata.readthedocs.io/en/latest/',
    'analytics_code': 'None',
    'single_version': False,
    'conf_py_path': '/docs/',
    'api_host': 'https://readthedocs.com',
    'github_user': 'scverse',
    'proxied_api_host': '/_',
    'github_repo': 'anndata',
    'github_version': 'd856f9b9da34975d2f60eea852051fc14b6c35db',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'd856f9b9da34975d2f60eea852051fc14b6c35db',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'd856f9b9da34975d2f60eea852051fc14b6c35db',
    'display_gitlab': False,
    'READTHEDOCS': True,
    'using_theme': (html_theme == "default"),
    'new_theme': (html_theme == "sphinx_rtd_theme"),
    'source_suffix': SUFFIX,
    'ad_free': False,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': 'd856f9b9',
}

# For sphinx >=1.8 we can use html_baseurl to set the canonical URL.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl
if version_info >= (1, 8):
    if not globals().get('html_baseurl'):
        html_baseurl = context['canonical_url']
    context['canonical_url'] = None





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 'external' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'https://github.com/scverse/anndata/pull/947'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/1461741/'

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'

# Make sure our build directory is always excluded
exclude_patterns = globals().get('exclude_patterns', [])
exclude_patterns.extend(['_build'])