Read the Docs build information
Build id: 2037679
Project: icb-scanpy
Version: latest
Commit: 29a6e3eda38dfcc8c3da01ec5619cc5a2e06025f
Date: 2024-02-23T07:56:48.986042Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-02-23T07:56:50.097924Z, end-time: 2024-02-23T07:56:51.607429Z, duration: 1, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-02-23T07:56:51.674288Z, end-time: 2024-02-23T07:56:52.752838Z, duration: 1, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 refs/heads/master:refs/remotes/origin/master
From https://github.com/scverse/scanpy
 * [new tag]         1.10.0rc1  -> 1.10.0rc1

[rtd-command-info] start-time: 2024-02-23T07:56:52.883470Z, end-time: 2024-02-23T07:56:53.102559Z, duration: 0, exit-code: 0
git checkout --force origin/master
Note: switching to '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 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 29a6e3e Fix pytest deprecation warning (#2879)

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git clean -d -f -f


[rtd-command-info] start-time: 2024-02-23T07:56:53.317183Z, end-time: 2024-02-23T07:56:53.374960Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-20.04
  tools:
    python: '3.12'
sphinx:
  fail_on_warning: true # do not change or you will be fired
  configuration: docs/conf.py
python:
  install:
  - method: pip
    path: .
    extra_requirements:
    - doc
    - leiden

[rtd-command-info] start-time: 2024-02-23T07:56:59.775576Z, end-time: 2024-02-23T07:56:59.853983Z, duration: 0, exit-code: 0
asdf global python 3.12.0


[rtd-command-info] start-time: 2024-02-23T07:57:00.266231Z, end-time: 2024-02-23T07:57:01.418752Z, duration: 1, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.0.final.0-64 in 836ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest, 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: 2024-02-23T07:57:01.497217Z, end-time: 2024-02-23T07:57:15.296240Z, duration: 13, 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-scanpy/envs/latest/lib/python3.12/site-packages (23.1)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.12/site-packages (67.6.1)
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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-24.0 setuptools-69.1.0

[rtd-command-info] start-time: 2024-02-23T07:57:15.378196Z, end-time: 2024-02-23T07:57:22.452038Z, 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, 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 Jinja2-3.1.3 MarkupSafe-2.1.5 Pygments-2.17.2 alabaster-0.7.16 babel-2.14.0 certifi-2024.2.2 charset-normalizer-3.3.2 docutils-0.20.1 idna-3.6 imagesize-1.4.1 packaging-23.2 readthedocs-sphinx-ext-2.2.5 requests-2.31.0 snowballstemmer-2.2.0 sphinx-7.2.6 sphinxcontrib-applehelp-1.0.8 sphinxcontrib-devhelp-1.0.6 sphinxcontrib-htmlhelp-2.0.5 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.7 sphinxcontrib-serializinghtml-1.1.10 urllib3-2.2.1

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .[doc,leiden]
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
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Collecting anndata>=0.8 (from scanpy==1.10.0rc2.dev1+g29a6e3e)
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Collecting legacy-api-wrap>=1.4 (from scanpy==1.10.0rc2.dev1+g29a6e3e)
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Collecting matplotlib>=3.6 (from scanpy==1.10.0rc2.dev1+g29a6e3e)
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Building wheels for collected packages: scanpy, umap-learn, sam-algorithm, session-info, hnswlib
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  Building wheel for scanpy (pyproject.toml): finished with status 'done'
  Created wheel for scanpy: filename=scanpy-1.10.0rc2.dev1+g29a6e3e-py3-none-any.whl size=2075662 sha256=d260123650dabeb4b4341f66f999c4db4dbd40d5716d21eeb6d337bd09096922
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Successfully built scanpy umap-learn sam-algorithm session-info hnswlib
Installing collected packages: webencodings, wcwidth, texttable, pytz, pure-eval, ptyprocess, fastjsonschema, zipp, tzdata, typing-extensions, traitlets, tqdm, tornado, toolz, tinycss2, threadpoolctl, tabulate, stdlib_list, soupsieve, six, rpds-py, readthedocs-sphinx-search, pyzmq, pyyaml, pyparsing, psutil, prompt-toolkit, platformdirs, pillow, pexpect, parso, pandocfilters, numpy, networkx, nest-asyncio, natsort, mistune, mdurl, locket, llvmlite, legacy-api-wrap, kiwisolver, jupyterlab-pygments, joblib, igraph, greenlet, fsspec, fonttools, executing, dill, defusedxml, decorator, debugpy, cycler, cloudpickle, click, attrs, array-api-compat, accessible-pygments, sqlalchemy, session-info, scipy, referencing, python-dateutil, patsy, partd, numba, matplotlib-inline, markdown-it-py, leidenalg, jupyter-core, jedi, importlib_metadata, hnswlib, h5py, contourpy, comm, bleach, beautifulsoup4, asttokens, stack-data, sphinxext-opengraph, sphinx-design, sphinx-copybutton, sphinx-autodoc-typehints, scikit-learn, scanpydoc, pydata-sphinx-theme, pandas, mdit-py-plugins, matplotlib, jupyter-client, jsonschema-specifications, dask, statsmodels, sphinx-book-theme, seaborn, pynndescent, myst-parser, jsonschema, ipython, harmonypy, anndata, umap-learn, nbformat, ipykernel, scanpy, sam-algorithm, nbclient, nbconvert, jupyter-cache, nbsphinx, myst-nb
Successfully installed accessible-pygments-0.0.4 anndata-0.10.5.post1 array-api-compat-1.4.1 asttokens-2.4.1 attrs-23.2.0 beautifulsoup4-4.12.3 bleach-6.1.0 click-8.1.7 cloudpickle-3.0.0 comm-0.2.1 contourpy-1.2.0 cycler-0.12.1 dask-2024.2.0 debugpy-1.8.1 decorator-5.1.1 defusedxml-0.7.1 dill-0.3.8 executing-2.0.1 fastjsonschema-2.19.1 fonttools-4.49.0 fsspec-2024.2.0 greenlet-3.0.3 h5py-3.10.0 harmonypy-0.0.9 hnswlib-0.8.0 igraph-0.11.4 importlib_metadata-7.0.1 ipykernel-6.29.2 ipython-8.22.1 jedi-0.19.1 joblib-1.3.2 jsonschema-4.21.1 jsonschema-specifications-2023.12.1 jupyter-cache-1.0.0 jupyter-client-8.6.0 jupyter-core-5.7.1 jupyterlab-pygments-0.3.0 kiwisolver-1.4.5 legacy-api-wrap-1.4 leidenalg-0.10.2 llvmlite-0.42.0 locket-1.0.0 markdown-it-py-3.0.0 matplotlib-3.8.3 matplotlib-inline-0.1.6 mdit-py-plugins-0.4.0 mdurl-0.1.2 mistune-3.0.2 myst-nb-1.0.0 myst-parser-2.0.0 natsort-8.4.0 nbclient-0.9.0 nbconvert-7.16.1 nbformat-5.9.2 nbsphinx-0.9.3 nest-asyncio-1.6.0 networkx-3.2.1 numba-0.59.0 numpy-1.26.4 pandas-2.2.0 pandocfilters-1.5.1 parso-0.8.3 partd-1.4.1 patsy-0.5.6 pexpect-4.9.0 pillow-10.2.0 platformdirs-4.2.0 prompt-toolkit-3.0.43 psutil-5.9.8 ptyprocess-0.7.0 pure-eval-0.2.2 pydata-sphinx-theme-0.15.2 pynndescent-0.5.11 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2024.1 pyyaml-6.0.1 pyzmq-25.1.2 readthedocs-sphinx-search-0.3.2 referencing-0.33.0 rpds-py-0.18.0 sam-algorithm-1.0.2 scanpy-1.10.0rc2.dev1+g29a6e3e scanpydoc-0.13.4 scikit-learn-1.4.1.post1 scipy-1.12.0 seaborn-0.13.2 session-info-1.0.0 six-1.16.0 soupsieve-2.5 sphinx-autodoc-typehints-2.0.0 sphinx-book-theme-1.1.2 sphinx-copybutton-0.5.2 sphinx-design-0.5.0 sphinxext-opengraph-0.9.1 sqlalchemy-2.0.27 stack-data-0.6.3 statsmodels-0.14.1 stdlib_list-0.10.0 tabulate-0.9.0 texttable-1.7.0 threadpoolctl-3.3.0 tinycss2-1.2.1 toolz-0.12.1 tornado-6.4 tqdm-4.66.2 traitlets-5.14.1 typing-extensions-4.9.0 tzdata-2024.1 umap-learn-0.5.5 wcwidth-0.2.13 webencodings-0.5.1 zipp-3.17.0

[rtd-command-info] start-time: 2024-02-23T07:59:15.220538Z, end-time: 2024-02-23T07:59:15.279027Z, duration: 0, exit-code: 0
cat docs/conf.py
from __future__ import annotations

import sys
from datetime import datetime
from pathlib import Path
from typing import TYPE_CHECKING

import matplotlib  # noqa
from packaging.version import Version

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

HERE = Path(__file__).parent
sys.path[:0] = [str(HERE.parent), str(HERE / "extensions")]
import scanpy  # noqa

if TYPE_CHECKING:
    from sphinx.application import Sphinx


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


nitpicky = True  # Warn about broken links. This is here for a reason: Do not change.
needs_sphinx = "4.0"  # Nicer param docs
suppress_warnings = [
    "myst.header",  # https://github.com/executablebooks/MyST-Parser/issues/262
]

# General information
project = "Scanpy"
author = "Scanpy development team"
repository_url = "https://github.com/scverse/scanpy"
copyright = f"{datetime.now():%Y}, the Scanpy development team."
version = scanpy.__version__.replace(".dirty", "")

# Bumping the version updates all docs, so don't do that
if Version(version).is_devrelease:
    parsed = Version(version)
    version = f"{parsed.major}.{parsed.minor}.{parsed.micro}.dev"

release = version

# default settings
templates_path = ["_templates"]
master_doc = "index"
default_role = "literal"
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints"]

extensions = [
    "myst_nb",
    "sphinx_copybutton",
    "sphinx.ext.autodoc",
    "sphinx.ext.intersphinx",
    "sphinx.ext.doctest",
    "sphinx.ext.coverage",
    "sphinx.ext.mathjax",
    "sphinx.ext.napoleon",
    "sphinx.ext.autosummary",
    "sphinx.ext.extlinks",
    "matplotlib.sphinxext.plot_directive",
    "sphinx_autodoc_typehints",  # needs to be after napoleon
    "git_ref",  # needs to be before scanpydoc.rtd_github_links
    "scanpydoc",  # needs to be before sphinx.ext.linkcode
    "sphinx.ext.linkcode",
    "sphinx_design",
    "sphinx_search.extension",
    "sphinxext.opengraph",
    *[p.stem for p in (HERE / "extensions").glob("*.py") if p.stem not in {"git_ref"}],
]

# 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
api_dir = HERE / "api"  # function_images
myst_enable_extensions = [
    "amsmath",
    "colon_fence",
    "deflist",
    "dollarmath",
    "html_image",
    "html_admonition",
]
myst_url_schemes = ("http", "https", "mailto")
nb_output_stderr = "remove"
nb_execution_mode = "off"
nb_merge_streams = True


ogp_site_url = "https://scanpy.readthedocs.io/en/stable/"
ogp_image = "https://scanpy.readthedocs.io/en/stable/_static/Scanpy_Logo_BrightFG.svg"

typehints_defaults = "braces"

pygments_style = "default"
pygments_dark_style = "native"

intersphinx_mapping = dict(
    anndata=("https://anndata.readthedocs.io/en/stable/", None),
    bbknn=("https://bbknn.readthedocs.io/en/latest/", None),
    cuml=("https://docs.rapids.ai/api/cuml/stable/", None),
    cycler=("https://matplotlib.org/cycler/", None),
    dask=("https://docs.dask.org/en/stable/", None),
    dask_ml=("https://ml.dask.org/", None),
    h5py=("https://docs.h5py.org/en/stable/", None),
    ipython=("https://ipython.readthedocs.io/en/stable/", None),
    igraph=("https://python.igraph.org/en/stable/api/", None),
    leidenalg=("https://leidenalg.readthedocs.io/en/latest/", None),
    louvain=("https://louvain-igraph.readthedocs.io/en/latest/", None),
    matplotlib=("https://matplotlib.org/stable/", None),
    networkx=("https://networkx.org/documentation/stable/", None),
    numpy=("https://numpy.org/doc/stable/", None),
    pandas=("https://pandas.pydata.org/pandas-docs/stable/", None),
    pynndescent=("https://pynndescent.readthedocs.io/en/latest/", None),
    pytest=("https://docs.pytest.org/en/latest/", None),
    python=("https://docs.python.org/3", None),
    rapids_singlecell=("https://rapids-singlecell.readthedocs.io/en/latest/", None),
    scipy=("https://docs.scipy.org/doc/scipy/", None),
    seaborn=("https://seaborn.pydata.org/", None),
    sklearn=("https://scikit-learn.org/stable/", None),
    tutorials=("https://scanpy-tutorials.readthedocs.io/en/latest/", None),
)


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

# The theme is sphinx-book-theme, with patches for readthedocs-sphinx-search
html_theme = "scanpydoc"
html_theme_options = {
    "repository_url": repository_url,
    "use_repository_button": True,
}
html_static_path = ["_static"]
html_show_sphinx = False
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"
html_title = "scanpy"


def setup(app: Sphinx):
    """App setup hook."""
    app.add_config_value(
        "recommonmark_config",
        {
            "auto_toc_tree_section": "Contents",
            "enable_auto_toc_tree": True,
            "enable_math": True,
            "enable_inline_math": False,
            "enable_eval_rst": True,
        },
        True,
    )


# -- 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",
    )
]


# -- Suppress link warnings ----------------------------------------------------

qualname_overrides = {
    "sklearn.neighbors._dist_metrics.DistanceMetric": "sklearn.metrics.DistanceMetric",
    "scanpy.plotting._matrixplot.MatrixPlot": "scanpy.pl.MatrixPlot",
    "scanpy.plotting._dotplot.DotPlot": "scanpy.pl.DotPlot",
    "scanpy.plotting._stacked_violin.StackedViolin": "scanpy.pl.StackedViolin",
    "pandas.core.series.Series": "pandas.Series",
}

nitpick_ignore = [
    # Technical issues
    ("py:class", "numpy.int64"),  # documented as “attribute”
    # Will probably be documented
    ("py:class", "scanpy._settings.Verbosity"),
    ("py:class", "scanpy.neighbors.OnFlySymMatrix"),
    ("py:class", "scanpy.plotting._baseplot_class.BasePlot"),
    # Currently undocumented
    # https://github.com/mwaskom/seaborn/issues/1810
    ("py:class", "seaborn.matrix.ClusterGrid"),
    ("py:class", "samalg.SAM"),
    # Won’t be documented
    ("py:class", "scanpy.plotting._utils._AxesSubplot"),
    ("py:class", "scanpy._utils.Empty"),
    ("py:class", "numpy.random.mtrand.RandomState"),
    ("py:class", "scanpy.neighbors._types.KnnTransformerLike"),
    # Will work once scipy 1.8 is released
    ("py:class", "scipy.sparse.base.spmatrix"),
    ("py:class", "scipy.sparse.csr.csr_matrix"),
]

# Options for plot examples

plot_include_source = True
plot_formats = [("png", 90)]
plot_html_show_formats = False
plot_html_show_source_link = False
plot_working_directory = HERE.parent  # Project root

# extlinks config
extlinks = {
    "issue": ("https://github.com/scverse/scanpy/issues/%s", "issue%s"),
    "pr": ("https://github.com/scverse/scanpy/pull/%s", "pr%s"),
}




###########################################################################
#          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': "latest",
    'version_slug': "latest",
    '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/"),
    ("1.9.x", "/en/1.9.x/"),
    ("1.8.x", "/en/1.8.x/"),
    ("1.7.x", "/en/1.7.x/"),
    ("1.6.x", "/en/1.6.x/"),
    ],
    'downloads': [ 
    ],
    'subprojects': [ 
    ],
    'slug': 'icb-scanpy',
    'name': u'scanpy',
    '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': '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,
    'docsearch_disabled': False,
    'user_analytics_code': '',
    'global_analytics_code': 'UA-17997319-2',
    'commit': '29a6e3ed',
}

# 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-scanpy/builds/2037679/'

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: 2024-02-23T07:59:15.350509Z, end-time: 2024-02-23T08:03:55.145793Z, duration: 279, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v7.2.6
Matplotlib is building the font cache; this may take a moment.
making output directory... done
myst v2.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'html_image', 'colon_fence', 'html_admonition', 'amsmath', 'deflist', 'dollarmath'}, disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.0.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', execution_mode='off', execution_cache_path='', execution_excludepatterns=(), execution_timeout=30, execution_in_temp=False, execution_allow_errors=False, execution_raise_on_error=False, execution_show_tb=False, merge_streams=True, render_plugin='default', remove_code_source=False, remove_code_outputs=False, code_prompt_show='Show code cell {type}', code_prompt_hide='Hide code cell {type}', number_source_lines=False, output_stderr='remove', render_text_lexer='myst-ansi', render_error_lexer='ipythontb', render_image_options={}, render_figure_options={}, render_markdown_format='commonmark', output_folder='build', append_css=True, metadata_to_fm=False)
Using jupyter-cache at: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/_readthedocs/.jupyter_cache
loading intersphinx inventory from https://anndata.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://bbknn.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://docs.rapids.ai/api/cuml/stable/objects.inv...
loading intersphinx inventory from https://matplotlib.org/cycler/objects.inv...
loading intersphinx inventory from https://docs.dask.org/en/stable/objects.inv...
loading intersphinx inventory from https://ml.dask.org/objects.inv...
loading intersphinx inventory from https://docs.h5py.org/en/stable/objects.inv...
loading intersphinx inventory from https://ipython.readthedocs.io/en/stable/objects.inv...
loading intersphinx inventory from https://python.igraph.org/en/stable/api/objects.inv...
loading intersphinx inventory from https://leidenalg.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://louvain-igraph.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://matplotlib.org/stable/objects.inv...
loading intersphinx inventory from https://networkx.org/documentation/stable/objects.inv...
loading intersphinx inventory from https://numpy.org/doc/stable/objects.inv...
loading intersphinx inventory from https://pandas.pydata.org/pandas-docs/stable/objects.inv...
loading intersphinx inventory from https://pynndescent.readthedocs.io/en/latest/objects.inv...
loading intersphinx inventory from https://docs.pytest.org/en/latest/objects.inv...
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
loading intersphinx inventory from https://rapids-singlecell.readthedocs.io/en/latest/objects.inv...
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loading intersphinx inventory from https://seaborn.pydata.org/objects.inv...
loading intersphinx inventory from https://scikit-learn.org/stable/objects.inv...
loading intersphinx inventory from https://scanpy-tutorials.readthedocs.io/en/latest/objects.inv...
[autosummary] generating autosummary for: _tutorials.md, api/classes.md, api/datasets.md, api/deprecated.md, api/experimental.md, api/get.md, api/index.md, api/metrics.md, api/plotting.md, api/preprocessing.md, ..., release-notes/1.9.1.md, release-notes/1.9.2.md, release-notes/1.9.3.md, release-notes/1.9.4.md, release-notes/1.9.5.md, release-notes/1.9.6.md, release-notes/1.9.7.md, release-notes/1.9.8.md, release-notes/index.md, usage-principles.md
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.MatrixPlot.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.StackedViolin.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.diffmap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_groups_pseudotime.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.dpt_timeseries.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.draw_graph.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.embedding_density.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/scanpy.pl.filter_genes_dispersion.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.leiden.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.louvain.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.marker_gene_overlap.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.paga.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.rank_genes_groups.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.score_genes_cell_cycle.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.sim.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.tsne.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy.tl.umap.rst
[autosummary] generating autosummary for: /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_HEIGHT.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_CATEGORY_WIDTH.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLORMAP.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_LEGEND_TITLE.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_COLOR_ON.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGECOLOR.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_EDGELW.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MAX.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_DOT_MIN.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/api/generated/classes/scanpy.pl.DotPlot.DEFAULT_LARGEST_DOT.rst, ..., /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_data.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.file_format_figs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logfile.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.logpath.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.max_memory.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.n_jobs.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.plot_suffix.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.set_figure_params.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.verbosity.rst, /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/checkouts/latest/docs/generated/scanpy._settings.ScanpyConfig.writedir.rst
The default value for `navigation_with_keys` will change to `False` in the next release. If you wish to preserve the old behavior for your site, set `navigation_with_keys=True` in the `html_theme_options` dict in your `conf.py` file. Be aware that `navigation_with_keys = True` has negative accessibility implications: https://github.com/pydata/pydata-sphinx-theme/issues/1492
building [mo]: targets for 0 po files that are out of date
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building [html]: targets for 82 source files that are out of date
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/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy/envs/latest/lib/python3.12/site-packages/anndata/_core/anndata.py:1906: UserWarning: Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
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dumping search index in English (code: en)... done
dumping object inventory... done
Updating searchtools for Read the Docs search... build succeeded.

The HTML pages are in ../_readthedocs/html.