Read the Docs build information
Build id: 2439782
Project: icb-anndata
Version: 1604
Commit: b5bbf0979143395f70b3ed32be81e250df0787be
Date: 2024-08-26T13:47:24.220718Z
State: cancelled
Success: False


[rtd-command-info] start-time: 2024-08-26T13:47:25.371271Z, end-time: 2024-08-26T13:47:25.946136Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-08-26T13:47:26.024118Z, end-time: 2024-08-26T13:47:26.549216Z, duration: 0, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/1604/head:external-1604
From https://github.com/scverse/anndata
 * [new ref]         refs/pull/1604/head -> external-1604

[rtd-command-info] start-time: 2024-08-26T13:47:26.684544Z, end-time: 2024-08-26T13:47:26.760999Z, duration: 0, exit-code: 0
git checkout --force b5bbf0979143395f70b3ed32be81e250df0787be
Note: switching to 'b5bbf0979143395f70b3ed32be81e250df0787be'.

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 b5bbf09 Merge branch 'main' into ig/towncrier

[rtd-command-info] start-time: 2024-08-26T13:47:26.831799Z, end-time: 2024-08-26T13:47:26.890837Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: "3.12"
sphinx:
  configuration: docs/conf.py
  fail_on_warning: true # do not change or you will be fired
python:
  install:
    - method: pip
      path: .
      extra_requirements:
        - doc
submodules:
  include:
    - "docs/tutorials/notebooks"
  recursive: true

[rtd-command-info] start-time: 2024-08-26T13:47:27.028529Z, end-time: 2024-08-26T13:47:27.109883Z, duration: 0, exit-code: 0
git submodule sync


[rtd-command-info] start-time: 2024-08-26T13:47:27.181649Z, end-time: 2024-08-26T13:47:27.750584Z, duration: 0, exit-code: 0
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/1604/docs/tutorials/notebooks'...
Submodule path 'docs/tutorials/notebooks': checked out '9e186c5c694793bb04ea1397721d154d6e0b7069'

[rtd-command-info] start-time: 2024-08-26T13:47:33.937083Z, end-time: 2024-08-26T13:47:34.018417Z, duration: 0, exit-code: 0
asdf global python 3.12.3


[rtd-command-info] start-time: 2024-08-26T13:47:34.423517Z, end-time: 2024-08-26T13:47:35.639023Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 866ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/1604, 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==23.1, setuptools==67.6.1, wheel==0.40.0
  activators BashActivator,CShellActivator,FishActivator,NushellActivator,PowerShellActivator,PythonActivator

[rtd-command-info] start-time: 2024-08-26T13:47:35.711097Z, end-time: 2024-08-26T13:47:50.001482Z, duration: 14, 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/1604/lib/python3.12/site-packages (23.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
    Found existing installation: setuptools 67.6.1
    Uninstalling setuptools-67.6.1:
      Successfully uninstalled setuptools-67.6.1
  Attempting uninstall: pip
    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.2 setuptools-73.0.1

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python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx, readthedocs-sphinx-ext
Successfully installed Jinja2-3.1.4 MarkupSafe-2.1.5 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.7.4 charset-normalizer-3.3.2 docutils-0.21.2 idna-3.8 imagesize-1.4.1 packaging-24.1 readthedocs-sphinx-ext-2.2.5 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.0.2 sphinxcontrib-applehelp-2.0.0 sphinxcontrib-devhelp-2.0.0 sphinxcontrib-htmlhelp-2.1.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-2.0.0 sphinxcontrib-serializinghtml-2.0.0 urllib3-2.2.2

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/checkouts/1604
  Installing build dependencies: started
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Building wheels for collected packages: anndata, asciitree
  Building wheel for anndata (pyproject.toml): started
  Building wheel for anndata (pyproject.toml): finished with status 'done'
  Created wheel for anndata: filename=anndata-0.1.dev69+gb5bbf09-py3-none-any.whl size=137043 sha256=ae73a844f2c91e5c5c195c56072aecc7dd89f9c967671f43992d5551e0bc8ba8
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Successfully built anndata asciitree
Installing collected packages: webencodings, wcwidth, pytz, pure-eval, ptyprocess, fastjsonschema, asciitree, array-api-compat, tzdata, typing-extensions, traitlets, tornado, tinycss2, tabulate, soupsieve, six, ruamel.yaml.clib, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, prompt-toolkit, platformdirs, pexpect, parso, pandocfilters, numpy, natsort, msgpack, more-itertools, mistune, mdurl, jupyterlab-pygments, fsspec, filelock, fasteners, executing, defusedxml, decorator, attrs, accessible-pygments, sphinx-jinja2-compat, scipy, ruamel.yaml, referencing, python-dateutil, numcodecs, matplotlib-inline, markdown-it-py, jupyter-core, jedi, html5lib, h5py, domdf-python-tools, cssutils, cachecontrol, bleach, beautifulsoup4, awkward-cpp, asttokens, zarr, stack-data, sphinxext-opengraph, sphinx-tabs, sphinx-prompt, sphinx-issues, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, jupyter-client, jsonschema-specifications, dict2css, awkward, autodocsumm, apeye-core, sphinx-book-theme, myst-parser, jsonschema, ipython, apeye, anndata, sphinx-toolbox, nbformat, nbclient, nbconvert, nbsphinx
Successfully installed accessible-pygments-0.0.5 anndata-0.1.dev69+gb5bbf09 apeye-1.4.1 apeye-core-1.1.5 array-api-compat-1.8 asciitree-0.3.3 asttokens-2.4.1 attrs-24.2.0 autodocsumm-0.2.13 awkward-2.6.7 awkward-cpp-37 beautifulsoup4-4.12.3 bleach-6.1.0 cachecontrol-0.14.0 cssutils-2.11.1 decorator-5.1.1 defusedxml-0.7.1 dict2css-0.3.0.post1 domdf-python-tools-3.9.0 executing-2.0.1 fasteners-0.19 fastjsonschema-2.20.0 filelock-3.15.4 fsspec-2024.6.1 h5py-3.11.0 html5lib-1.1 ipython-8.26.0 jedi-0.19.1 jsonschema-4.23.0 jsonschema-specifications-2023.12.1 jupyter-client-8.6.2 jupyter-core-5.7.2 jupyterlab-pygments-0.3.0 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.1 mdurl-0.1.2 mistune-3.0.2 more-itertools-10.4.0 msgpack-1.0.8 myst-parser-4.0.0 natsort-8.4.0 nbclient-0.10.0 nbconvert-7.16.4 nbformat-5.10.4 nbsphinx-0.9.5 numcodecs-0.13.0 numpy-2.1.0 pandas-2.2.2 pandocfilters-1.5.1 parso-0.8.4 pexpect-4.9.0 platformdirs-4.2.2 prompt-toolkit-3.0.47 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.15.4 python-dateutil-2.9.0.post0 pytz-2024.1 pyyaml-6.0.2 pyzmq-26.2.0 readthedocs-sphinx-search-0.3.2 referencing-0.35.1 rpds-py-0.20.0 ruamel.yaml-0.18.6 ruamel.yaml.clib-0.2.8 scanpydoc-0.13.6 scipy-1.14.1 six-1.16.0 soupsieve-2.6 sphinx-autodoc-typehints-2.2.3 sphinx-book-theme-1.1.3 sphinx-copybutton-0.5.2 sphinx-design-0.6.1 sphinx-issues-4.1.0 sphinx-jinja2-compat-0.3.0 sphinx-prompt-1.9.0 sphinx-tabs-3.4.5 sphinx-toolbox-3.8.0 sphinxext-opengraph-0.9.1 stack-data-0.6.3 tabulate-0.9.0 tinycss2-1.3.0 tornado-6.4.1 traitlets-5.14.3 typing-extensions-4.12.2 tzdata-2024.1 wcwidth-0.2.13 webencodings-0.5.1 zarr-2.18.2

[rtd-command-info] start-time: 2024-08-26T13:48:38.549630Z, end-time: 2024-08-26T13:48:38.606793Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

import sys
from datetime import datetime
from functools import partial
from importlib import metadata
from pathlib import Path, PurePosixPath
from typing import TYPE_CHECKING

from docutils import nodes

if TYPE_CHECKING:
    from sphinx.application import Sphinx

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE / "extensions")]


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

# General information
project = "anndata"
author = f"{project} developers"
copyright = f"{datetime.now():%Y}, {author}"
release = version = metadata.version("anndata")

# default settings
templates_path = ["_templates"]
html_static_path = ["_static"]
source_suffix = {".rst": "restructuredtext", ".md": "markdown"}
master_doc = "index"
default_role = "literal"
exclude_patterns = [
    "_build",
    "Thumbs.db",
    ".DS_Store",
    "**.ipynb_checkpoints",
    "tutorials/notebooks/*.rst",
    # exclude all 0.x.y.md files, but not index.md
    "release-notes/[!i]*.md",
    "news.md",  # is `include`d into index.md
]
pygments_style = "sphinx"

extensions = [
    "myst_parser",
    "sphinx_copybutton",
    "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",
    "sphinx_design",
    "sphinx_search.extension",
    "sphinxext.opengraph",
    "scanpydoc",  # needs to be before linkcode
    "sphinx.ext.linkcode",
    "nbsphinx",
    "IPython.sphinxext.ipython_console_highlighting",
    "patch_sphinx_toolbox_autoprotocol",  # internal extension
    "sphinx_toolbox.more_autodoc.autoprotocol",
    # other internal extensions
    "patch_myst_cite",
    "release_notes",
]
myst_enable_extensions = [
    "html_image",  # So README.md can be used on github and sphinx docs
]
myst_heading_anchors = 3

# Generate the API documentation when building
autosummary_generate = True
autodoc_member_order = "bysource"
issues_github_path = "scverse/anndata"
rtd_links_prefix = PurePosixPath("src")
# 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"]
    ],
    # TODO: sphinx’ builtin autodoc.typehints extension isn’t handled by `qualname_overrides` yet
    # https://github.com/theislab/scanpydoc/issues/140
    ("py:class", "h5py._hl.group.Group"),
    ("py:class", "h5py._hl.dataset.Dataset"),
    # for experimental callback exports
    ("py:class", "anndata.compat.ZappyArray"),
    ("py:class", "anndata.compat.DaskArray"),
    ("py:class", "anndata.compat.CupyArray"),
    ("py:class", "anndata.compat.CupySparseMatrix"),
    ("py:class", "numpy.ma.core.MaskedArray"),
    ("py:class", "dask.array.core.Array"),
    ("py:class", "awkward.highlevel.Array"),
    ("py:class", "anndata._core.sparse_dataset.BaseCompressedSparseDataset"),
    ("py:obj", "numpy._typing._array_like._ScalarType_co"),
]


def setup(app: Sphinx):
    app.add_generic_role("small", partial(nodes.inline, classes=["small"]))
    app.add_generic_role("smaller", partial(nodes.inline, classes=["smaller"]))


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),
    dask=("https://docs.dask.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",
    "anndata._types.ReadCallback": "anndata.experimental.ReadCallback",
    "anndata._types.WriteCallback": "anndata.experimental.WriteCallback",
    "anndata._types.Read": "anndata.experimental.Read",
    "anndata._types.Write": "anndata.experimental.Write",
    "anndata._types.RWAble": "anndata.experimental.RWAble",
}
autodoc_type_aliases = dict(
    NDArray=":data:`~numpy.typing.NDArray`",
    RWAble=":data:`~anndata.experimental.RWAble`",
    **{
        f"{v}variantInMemoryType": ":data:`~anndata.experimental.InMemoryElem`"
        for v in ["In", "Co", "Contra"]
    },
)

# -- 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 ----------------------------------------------


# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = dict(
    use_repository_button=True,
    repository_url="https://github.com/scverse/anndata",
    repository_branch="main",
    navigation_with_keys=False,  # https://github.com/pydata/pydata-sphinx-theme/issues/1492
)
html_logo = "_static/img/anndata_schema.svg"
issues_github_path = "scverse/anndata"
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')

# Define this variable in case it's not defined by the user.
# It defaults to `alabaster` which is the default from Sphinx.
# https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_theme
html_theme = globals().get('html_theme', 'alabaster')

#Add project information to the template context.
context = {
    'html_theme': html_theme,
    'current_version': "1604",
    'version_slug': "1604",
    '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/"),
    ("0.10.x", "/en/0.10.x/"),
    ("0.9.x", "/en/0.9.x/"),
    ("0.8.x", "/en/0.8.x/"),
    ("0.7.x", "/en/0.7.x/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-anndata',
    'name': u'anndata',
    'rtd_language': u'en',
    'programming_language': u'py',
    'canonical_url': '',
    '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': 'b5bbf0979143395f70b3ed32be81e250df0787be',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': 'b5bbf0979143395f70b3ed32be81e250df0787be',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': 'b5bbf0979143395f70b3ed32be81e250df0787be',
    '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': 'b5bbf097',
}

# 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():
    for key in context:
        if key not in html_context:
            html_context[key] = context[key]
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/1604'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/2439782/'

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'])