Read the Docs build information
Build id: 4041415
Project: icb-scanpy-tutorials
Version: latest
Commit: e7dad889edbb505ccd3fa1bf83cfd95d4da33e51
Date: 2026-05-25T18:45:35.827833Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-05-25T18:45:36.594925Z, end-time: 2026-05-25T18:45:43.213884Z, duration: 6, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-05-25T18:45:43.292933Z, end-time: 2026-05-25T18:45:48.862339Z, duration: 5, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 HEAD
From https://github.com/scverse/scanpy-tutorials
 * branch            HEAD       -> FETCH_HEAD

[rtd-command-info] start-time: 2026-05-25T18:45:49.573871Z, end-time: 2026-05-25T18:45:49.609578Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-24.04
  tools:
    python: "3.13"
sphinx:
  configuration: conf.py
  fail_on_warning: true
python:
  install:
    - method: pip
      path: .

[rtd-command-info] start-time: 2026-05-25T18:45:54.071803Z, end-time: 2026-05-25T18:45:54.123619Z, duration: 0, exit-code: 0
asdf global python 3.13.9


[rtd-command-info] start-time: 2026-05-25T18:45:54.653478Z, end-time: 2026-05-25T18:45:55.262652Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.9.final.0-64 in 377ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/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: 2026-05-25T18:45:55.565638Z, end-time: 2026-05-25T18:46:00.182290Z, duration: 4, 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-tutorials/envs/latest/lib/python3.13/site-packages (23.1)
Collecting pip
  Downloading pip-26.1.1-py3-none-any.whl (1.8 MB)
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Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/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-26.1.1 setuptools-82.0.1

[rtd-command-info] start-time: 2026-05-25T18:46:00.277145Z, end-time: 2026-05-25T18:46:04.808351Z, duration: 4, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
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Downloading pygments-2.20.0-py3-none-any.whl (1.2 MB)
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Downloading requests-2.34.2-py3-none-any.whl (73 kB)
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Downloading idna-3.16-py3-none-any.whl (74 kB)
Downloading urllib3-2.7.0-py3-none-any.whl (131 kB)
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Downloading sphinxcontrib_qthelp-2.0.0-py3-none-any.whl (88 kB)
Downloading sphinxcontrib_serializinghtml-2.0.0-py3-none-any.whl (92 kB)
Installing collected packages: urllib3, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, snowballstemmer, roman-numerals, Pygments, packaging, MarkupSafe, imagesize, idna, docutils, charset_normalizer, certifi, babel, alabaster, requests, Jinja2, sphinx

Successfully installed Jinja2-3.1.6 MarkupSafe-3.0.3 Pygments-2.20.0 alabaster-1.0.0 babel-2.18.0 certifi-2026.5.20 charset_normalizer-3.4.7 docutils-0.22.4 idna-3.16 imagesize-2.0.0 packaging-26.2 requests-2.34.2 roman-numerals-4.1.0 snowballstemmer-3.1.0 sphinx-9.1.0 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 urllib3-2.7.0

[rtd-command-info] start-time: 2026-05-25T18:46:04.889067Z, end-time: 2026-05-25T18:46:16.452944Z, duration: 11, exit-code: 0
python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .
Processing ./.
  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
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting myst-nb (from scanpy-tutorials==0.1.dev50+ge7dad889e)
  Downloading myst_nb-1.4.0-py3-none-any.whl.metadata (4.8 kB)
Collecting scanpydoc>=0.13.4 (from scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+ge7dad889e)
  Downloading scanpydoc-0.17.3-py3-none-any.whl.metadata (2.6 kB)
Requirement already satisfied: sphinx in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from scanpy-tutorials==0.1.dev50+ge7dad889e) (9.1.0)
Collecting sphinx-design (from scanpy-tutorials==0.1.dev50+ge7dad889e)
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Collecting sphinx-book-theme>=1.1.0 (from scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+ge7dad889e)
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Requirement already satisfied: sphinxcontrib-devhelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.0.0)
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Requirement already satisfied: sphinxcontrib-qthelp>=1.0.6 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.0.0)
Requirement already satisfied: sphinxcontrib-serializinghtml>=1.1.9 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.0.0)
Requirement already satisfied: Jinja2>=3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (3.1.6)
Requirement already satisfied: Pygments>=2.17 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.20.0)
Requirement already satisfied: docutils<0.23,>=0.21 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (0.22.4)
Requirement already satisfied: snowballstemmer>=2.2 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (3.1.0)
Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.18.0)
Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (1.0.0)
Requirement already satisfied: imagesize>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.0.0)
Requirement already satisfied: requests>=2.30.0 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/latest/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+ge7dad889e) (2.34.2)
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Collecting pydata-sphinx-theme==0.16.1 (from sphinx-book-theme>=1.1.0->scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+ge7dad889e)
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Collecting beautifulsoup4 (from pydata-sphinx-theme==0.16.1->sphinx-book-theme>=1.1.0->scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+ge7dad889e)
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Building wheels for collected packages: scanpy-tutorials
  Building wheel for scanpy-tutorials (pyproject.toml): started
  Building wheel for scanpy-tutorials (pyproject.toml): finished with status 'done'
  Created wheel for scanpy-tutorials: filename=scanpy_tutorials-0.1.dev50+ge7dad889e-py3-none-any.whl size=2130 sha256=802696f5d965004e1dd0136a410574aa832a5ca214fef070c0237280870328c5
  Stored in directory: /tmp/pip-ephem-wheel-cache-k6zosei9/wheels/73/f7/8c/76731b29b775884f34c3ac7056114c55ce8ba77c3d651b6bbd
Successfully built scanpy-tutorials
Installing collected packages: pure-eval, ptyprocess, fastjsonschema, zipp, wcwidth, typing-extensions, traitlets, tornado, tabulate, soupsieve, six, rpds-py, pyzmq, pyyaml, psutil, platformdirs, pexpect, parso, nest-asyncio, mdurl, ipython-pygments-lexers, greenlet, executing, decorator, debugpy, comm, click, attrs, asttokens, accessible-pygments, stack_data, sqlalchemy, referencing, python-dateutil, prompt_toolkit, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, beautifulsoup4, sphinx-design, scanpydoc, pydata-sphinx-theme, mdit-py-plugins, jupyter-client, jsonschema-specifications, ipython, sphinx-book-theme, myst-parser, jsonschema, ipykernel, nbformat, nbclient, jupyter-cache, myst-nb, scanpy-tutorials

Successfully installed accessible-pygments-0.0.5 asttokens-3.0.1 attrs-26.1.0 beautifulsoup4-4.14.3 click-8.4.1 comm-0.2.3 debugpy-1.8.20 decorator-5.3.1 executing-2.2.1 fastjsonschema-2.21.2 greenlet-3.5.1 importlib_metadata-9.0.0 ipykernel-7.2.0 ipython-9.13.0 ipython-pygments-lexers-1.1.1 jedi-0.20.0 jsonschema-4.26.0 jsonschema-specifications-2025.9.1 jupyter-cache-1.0.1 jupyter-client-8.8.0 jupyter-core-5.9.1 markdown-it-py-4.2.0 matplotlib-inline-0.2.2 mdit-py-plugins-0.6.1 mdurl-0.1.2 myst-nb-1.4.0 myst-parser-5.1.0 nbclient-0.10.4 nbformat-5.10.4 nest-asyncio-1.6.0 parso-0.8.7 pexpect-4.9.0 platformdirs-4.9.6 prompt_toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.16.1 python-dateutil-2.9.0.post0 pyyaml-6.0.3 pyzmq-27.1.0 referencing-0.37.0 rpds-py-0.30.0 scanpy-tutorials-0.1.dev50+ge7dad889e scanpydoc-0.17.3 six-1.17.0 soupsieve-2.8.4 sphinx-book-theme-1.2.0 sphinx-design-0.7.0 sqlalchemy-2.0.50 stack_data-0.6.3 tabulate-0.10.0 tornado-6.5.5 traitlets-5.15.0 typing-extensions-4.15.0 wcwidth-0.7.0 zipp-4.1.0

[rtd-command-info] start-time: 2026-05-25T18:46:16.612164Z, end-time: 2026-05-25T18:46:16.653067Z, duration: 0, exit-code: 0
cat conf.py
from __future__ import annotations

import os
from datetime import UTC, datetime
from importlib.metadata import metadata
from types import MappingProxyType
from typing import TYPE_CHECKING, ClassVar

from docutils import nodes
from sphinx import addnodes
from sphinx.domains import Domain
from sphinx.errors import NoUri
from sphinx.ext.intersphinx import resolve_reference_in_inventory
from sphinx.util.docutils import SphinxDirective


if TYPE_CHECKING:
    from collections.abc import Mapping, Sequence

    from docutils.parsers.rst.states import Inliner
    from sphinx.application import Sphinx
    from sphinx.environment import BuildEnvironment


meta = metadata("scanpy-tutorials")
project = meta["Name"]
author = meta["Author"]
copyright = f"{datetime.now(UTC):%Y}, {author}"  # noqa: A001
release = version = meta["Version"]

extensions = ["myst_nb", "sphinx.ext.intersphinx", "sphinx_design"]
myst_enable_extensions = [
    "colon_fence",
]

templates_path = ["_templates"]
source_suffix = ".rst"
master_doc = "index"
language = "en"
exclude_patterns = ["_build", "Thumbs.db", ".DS_Store", "**.ipynb_checkpoints", "scanpy_workshop", ".*cache"]
pygments_style = "sphinx"

intersphinx_mapping = dict(
    anndata=("https://anndata.readthedocs.io/en/stable/", None),
    scanpy=("https://scanpy.readthedocs.io/en/latest/", None),
)
suppress_warnings = ["image.not_readable"]

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

html_theme = "scanpydoc"
html_theme_options = dict(
    repository_url="https://github.com/theislab/scanpy-tutorials",
    repository_branch="master",
    use_repository_button=True,
)
html_static_path = ["_static"]
# include a warning background on RTD for everything but PR builds
html_css_files = (
    ["css/warning.css"]
    if os.environ.get("READTHEDOCS") and os.environ.get("READTHEDOCS_VERSION_TYPE") != "external"
    else []
)
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"

# -- Notebook settings ----------------------------------------------------

nb_execution_mode = "off"
nb_output_stderr = "remove"
myst_heading_anchors = 3
suppress_warnings = [
    # paga-paul15.ipynb: /_static/img/tutorials/paga_planaria.png
    "image.not_readable",
    # application/vnd.microsoft.datawrangler.viewer.v0+json
    "mystnb.unknown_mime_type",
]


# Roles “implementing” {cite}`…` and {cite:p}`…`/{cite:t}`…`


def fake_cite(
    name: str,
    rawtext: str,
    text: str,
    lineno: int,
    inliner: Inliner,
    options: Mapping[str, object] = MappingProxyType({}),
    content: Sequence[str] = (),
) -> tuple[list[nodes.Node], list[str]]:
    del name, lineno, options, content
    msg = f"cite:{text}"
    return [
        inliner.document.reporter.info(msg),
        nodes.emphasis(rawtext, f"[{text}]"),
    ], []


class FakeDomain(Domain):
    name: ClassVar = "cite"
    roles: ClassVar = dict(p=fake_cite, t=fake_cite)


# Role linking to the canonical location in scanpy’s docs


MSG = (
    "Please access this document in its canonical location as the currently accessed page may not be rendered correctly"
)


class CanonicalTutorial(SphinxDirective):
    required_arguments = 1
    has_content = False

    def run(self) -> list[nodes.Node]:
        """\
        Return a banner with a link to the canonical location.

        If the reference cannot be found, crash the build.
        """
        text = self.arguments[0]
        ref = resolve_reference_in_inventory(
            self.env,
            "scanpy",
            addnodes.pending_xref("", reftype="doc", refdomain="std", reftarget=text),
            nodes.inline("", text),
        )
        if ref is None:
            msg = f"Reference to scanpy:{text} not found"
            raise self.warning(msg)
        desc = nodes.inline("", f"{MSG}: ")
        banner = nodes.danger(
            text,
            nodes.paragraph("", "", desc, ref),
            classes=["admonition", "caution"],
        )
        return [banner]


def missing_reference(
    app: Sphinx,
    env: BuildEnvironment,
    node: addnodes.pending_xref,
    contnode: nodes.TextElement,
) -> nodes.Node | None:
    del app, env, contnode
    # ignore known scanpy labels
    if node["reftarget"] in {
        "external-data-integration",
        "eco-data-integration",
        "pl-embeddings",
    } or node["reftarget"].startswith("/tutorials"):
        raise NoUri
    return None


def setup(app: Sphinx) -> None:
    app.add_domain(FakeDomain)
    app.add_role("cite", fake_cite)
    app.add_directive("canonical-tutorial", CanonicalTutorial)
    app.connect("missing-reference", missing_reference)

[rtd-command-info] start-time: 2026-05-25T18:46:16.740227Z, end-time: 2026-05-25T18:46:21.019702Z, duration: 4, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v9.1.0
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
myst v5.1.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, strikethrough_single_tilde=False, colon_fence_exact_match=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.4.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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=False, render_plugin='default', remove_code_source=False, remove_code_outputs=False, scroll_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-tutorials/checkouts/latest/_readthedocs/.jupyter_cache
loading intersphinx inventory 'anndata' from https://anndata.readthedocs.io/en/stable/objects.inv ...
loading intersphinx inventory 'scanpy' from https://scanpy.readthedocs.io/en/latest/objects.inv ...
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dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded.

The HTML pages are in _readthedocs/html.