Read the Docs build information
Build id: 1813062
Project: icb-anndata
Version: 0.8.x
Commit: e675901e80d03b40ae3d7885fd94fbfd9fda1ea3
Date: 2023-10-30T13:48:07.742881Z
State: finished
Success: False


[rtd-command-info] start-time: 2023-10-30T14:07:10.141618Z, end-time: 2023-10-30T14:07:10.946533Z, duration: 0, exit-code: 0
git clone --depth 1 https://github.com/scverse/anndata.git .
Cloning into '.'...

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git fetch origin --force --prune --prune-tags --depth 50 refs/heads/0.8.x:refs/remotes/origin/0.8.x
From https://github.com/scverse/anndata
 * [new branch]      0.8.x      -> origin/0.8.x
 * [new tag]         0.7.7      -> 0.7.7
 * [new tag]         0.7.8      -> 0.7.8
 * [new tag]         0.8.0      -> 0.8.0
 * [new tag]         0.8.0.dev0 -> 0.8.0.dev0
 * [new tag]         0.8.0rc1   -> 0.8.0rc1

[rtd-command-info] start-time: 2023-10-30T14:07:12.517764Z, end-time: 2023-10-30T14:07:12.598376Z, duration: 0, exit-code: 0
git checkout --force origin/0.8.x
Note: switching to 'origin/0.8.x'.

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 e675901 Backport PR #856: Fix order type (#858)

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git clean -d -f -f


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cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.9'
sphinx:
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc

[rtd-command-info] start-time: 2023-10-30T14:07:18.610233Z, end-time: 2023-10-30T14:07:18.712201Z, duration: 0, exit-code: 0
asdf global python 3.9.18


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.9.18.final.0-64 in 759ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x, 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

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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/0.8.x/lib/python3.9/site-packages (23.1)
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Installing collected packages: setuptools, pip
  Attempting uninstall: setuptools
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    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-23.3.1 setuptools-68.2.2

[rtd-command-info] start-time: 2023-10-30T14:07:32.622631Z, end-time: 2023-10-30T14:07:39.688713Z, duration: 7, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx readthedocs-sphinx-ext
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Installing collected packages: snowballstemmer, zipp, urllib3, sphinxcontrib-jsmath, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset-normalizer, certifi, babel, alabaster, requests, Jinja2, importlib-metadata, readthedocs-sphinx-ext, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, sphinx
Successfully installed Jinja2-3.1.2 MarkupSafe-2.1.3 Pygments-2.16.1 alabaster-0.7.13 babel-2.13.1 certifi-2023.7.22 charset-normalizer-3.3.1 docutils-0.20.1 idna-3.4 imagesize-1.4.1 importlib-metadata-6.8.0 packaging-23.2 readthedocs-sphinx-ext-2.2.3 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.7 sphinxcontrib-devhelp-1.0.5 sphinxcontrib-htmlhelp-2.0.4 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.6 sphinxcontrib-serializinghtml-1.1.9 urllib3-2.0.7 zipp-3.17.0

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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/0.8.x
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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-0.8.1.dev9+ge675901-py3-none-any.whl size=428645 sha256=5c62112544dafe3360008b05137aa0ebbd9cb20cadced693eccc42ac2ebfb4a6
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  Building wheel for asciitree (setup.py): started
  Building wheel for asciitree (setup.py): finished with status 'done'
  Created wheel for asciitree: filename=asciitree-0.3.3-py3-none-any.whl size=5034 sha256=4ef45321778a051a2c173d3fb74891d9a742267726932e461e803e56043eb9f4
  Stored in directory: /tmp/pip-ephem-wheel-cache-nl9a2zbm/wheels/07/00/bc/937e878be0d781a569792a1e0e5acf149e463d4536453ec978
Successfully built anndata asciitree
Installing collected packages: webencodings, pytz, fastjsonschema, asciitree, tzdata, traitlets, tornado, tinycss2, soupsieve, six, rpds-py, pyzmq, platformdirs, pandocfilters, numpy, natsort, mistune, jupyterlab-pygments, get-annotations, fasteners, docutils, defusedxml, attrs, scipy, referencing, python-dateutil, numcodecs, jupyter-core, h5py, bleach, beautifulsoup4, zarr, pandas, jupyter-client, jsonschema-specifications, jsonschema, anndata, nbformat, nbclient, nbconvert, sphinxcontrib-jquery, sphinx-rtd-theme, sphinx_issues, sphinx-autodoc-typehints, scanpydoc, nbsphinx
  Attempting uninstall: docutils
    Found existing installation: docutils 0.20.1
    Uninstalling docutils-0.20.1:
      Successfully uninstalled docutils-0.20.1
Successfully installed anndata-0.8.1.dev9+ge675901 asciitree-0.3.3 attrs-23.1.0 beautifulsoup4-4.12.2 bleach-6.1.0 defusedxml-0.7.1 docutils-0.18.1 fasteners-0.19 fastjsonschema-2.18.1 get-annotations-0.1.2 h5py-3.10.0 jsonschema-4.19.2 jsonschema-specifications-2023.7.1 jupyter-client-8.5.0 jupyter-core-5.5.0 jupyterlab-pygments-0.2.2 mistune-3.0.2 natsort-8.4.0 nbclient-0.8.0 nbconvert-7.10.0 nbformat-5.9.2 nbsphinx-0.9.3 numcodecs-0.12.1 numpy-1.26.1 pandas-2.1.2 pandocfilters-1.5.0 platformdirs-3.11.0 python-dateutil-2.8.2 pytz-2023.3.post1 pyzmq-25.1.1 referencing-0.30.2 rpds-py-0.10.6 scanpydoc-0.9.5 scipy-1.11.3 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-1.24.0 sphinx-rtd-theme-1.3.0 sphinx_issues-3.0.1 sphinxcontrib-jquery-4.1 tinycss2-1.2.1 tornado-6.3.3 traitlets-5.13.0 tzdata-2023.3 webencodings-0.5.1 zarr-2.16.1

[rtd-command-info] start-time: 2023-10-30T14:08:19.931069Z, end-time: 2023-10-30T14:08:19.992206Z, 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"
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",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "scanpydoc",
    "nbsphinx",
    *[p.stem for p in (HERE / "extensions").glob("*.py")],
]

# 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
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"]


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


intersphinx_mapping = dict(
    h5py=("https://docs.h5py.org/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",
    "anndata._core.anndata.AnnData": "anndata.AnnData",
}

# -- 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="master",  # 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')

# 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': "0.8.x",
    'version_slug': "0.8.x",
    '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': '0.8.x',
    'display_github': True,
    'bitbucket_user': 'None',
    'bitbucket_repo': 'None',
    'bitbucket_version': '0.8.x',
    'display_bitbucket': False,
    'gitlab_user': 'None',
    'gitlab_repo': 'None',
    'gitlab_version': '0.8.x',
    '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': 'e675901e',
}

# 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 'branch' == 'external':
    extensions.insert(1, "readthedocs_ext.external_version_warning")
    readthedocs_vcs_url = 'None'
    readthedocs_build_url = 'https://readthedocs.com/projects/icb-anndata/builds/1813062/'

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'])

[rtd-command-info] start-time: 2023-10-30T14:08:20.096128Z, end-time: 2023-10-30T14:08:22.000095Z, duration: 1, exit-code: 2
python -m sphinx -T -E -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
making output directory... done

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/theming.py", line 83, in __init__
    self.base = factory.create(inherit)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/theming.py", line 230, in create
    raise ThemeError(__('no theme named %r found (missing theme.conf?)') % name)
sphinx.errors.ThemeError: no theme named 'sphinx_book_theme' found (missing theme.conf?)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/cmd/build.py", line 293, in build_main
    app = Sphinx(args.sourcedir, args.confdir, args.outputdir,
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/application.py", line 272, in __init__
    self._init_builder()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/application.py", line 342, in _init_builder
    self.builder.init()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/builders/html/__init__.py", line 219, in init
    self.init_templates()
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/builders/html/__init__.py", line 270, in init_templates
    self.theme = theme_factory.create(themename)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/theming.py", line 232, in create
    return Theme(name, self.themes[name], factory=self)
  File "/home/docs/checkouts/readthedocs.org/user_builds/icb-anndata/envs/0.8.x/lib/python3.9/site-packages/sphinx/theming.py", line 85, in __init__
    raise ThemeError(__('no theme named %r found, inherited by %r') %
sphinx.errors.ThemeError: no theme named 'sphinx_book_theme' found, inherited by 'scanpydoc'

Theme error:
no theme named 'sphinx_book_theme' found, inherited by 'scanpydoc'