Read the Docs build information
Build id: 3814136
Project: icb-scanpy-tutorials
Version: 222
Commit: 216d96bae1a1b2ba747df7118ddf30cbb1069d1a
Date: 2026-03-09T18:05:17.015805Z
State: finished
Success: True


[rtd-command-info] start-time: 2026-03-09T18:05:17.734745Z, end-time: 2026-03-09T18:05:24.331783Z, duration: 6, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2026-03-09T18:05:24.416869Z, end-time: 2026-03-09T18:05:31.145207Z, duration: 6, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/222/head:external-222
From https://github.com/scverse/scanpy-tutorials
 * [new ref]         refs/pull/222/head -> external-222

[rtd-command-info] start-time: 2026-03-09T18:05:31.970844Z, end-time: 2026-03-09T18:05:32.296851Z, duration: 0, exit-code: 0
git checkout --force 216d96bae1a1b2ba747df7118ddf30cbb1069d1a
Note: switching to '216d96bae1a1b2ba747df7118ddf30cbb1069d1a'.

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 216d96b [pre-commit.ci] pre-commit autoupdate

[rtd-command-info] start-time: 2026-03-09T18:05:32.373019Z, end-time: 2026-03-09T18:05:32.409019Z, 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: 2026-03-09T18:05:37.560152Z, end-time: 2026-03-09T18:05:37.616471Z, duration: 0, exit-code: 0
asdf global python 3.13.3


[rtd-command-info] start-time: 2026-03-09T18:05:38.001890Z, end-time: 2026-03-09T18:05:38.503790Z, duration: 0, exit-code: 0
python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.13.3.final.0-64 in 280ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/222, 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: 2026-03-09T18:05:38.586946Z, end-time: 2026-03-09T18:05:41.800416Z, duration: 3, 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/222/lib/python3.13/site-packages (23.1)
Collecting pip
  Downloading pip-26.0.1-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/222/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
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      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-26.0.1 setuptools-82.0.1

[rtd-command-info] start-time: 2026-03-09T18:05:41.898200Z, end-time: 2026-03-09T18:05:46.211606Z, duration: 4, exit-code: 0
python -m pip install --upgrade --no-cache-dir sphinx
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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-2.19.2 alabaster-1.0.0 babel-2.18.0 certifi-2026.2.25 charset_normalizer-3.4.5 docutils-0.22.4 idna-3.11 imagesize-2.0.0 packaging-26.0 requests-2.32.5 roman-numerals-4.1.0 snowballstemmer-3.0.1 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 urllib3-2.6.3

[rtd-command-info] start-time: 2026-03-09T18:05:46.293681Z, end-time: 2026-03-09T18:05:56.401354Z, duration: 10, 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+g216d96bae)
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Collecting scanpydoc>=0.13.4 (from scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+g216d96bae)
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Collecting sphinx-design (from scanpy-tutorials==0.1.dev50+g216d96bae)
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Requirement already satisfied: Jinja2>=3.1 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/222/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+g216d96bae) (3.1.6)
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Requirement already satisfied: babel>=2.13 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/222/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+g216d96bae) (2.18.0)
Requirement already satisfied: alabaster>=0.7.14 in /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/222/lib/python3.13/site-packages (from sphinx->scanpy-tutorials==0.1.dev50+g216d96bae) (1.0.0)
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Collecting pydata-sphinx-theme==0.15.4 (from sphinx-book-theme>=1.1.0->scanpydoc[theme]>=0.13.4->scanpy-tutorials==0.1.dev50+g216d96bae)
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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+g216d96bae-py3-none-any.whl size=2131 sha256=353a5780c873aeb15b4246b7e82147f7697fab38cd9edb6ec41294028a86dc80
  Stored in directory: /tmp/pip-ephem-wheel-cache-263jafl7/wheels/07/b8/44/03116a6045dcf2c3b9141e61066cb3fa4904c88989c908dee3
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-25.4.0 beautifulsoup4-4.14.3 click-8.3.1 comm-0.2.3 debugpy-1.8.20 decorator-5.2.1 executing-2.2.1 fastjsonschema-2.21.2 greenlet-3.3.2 importlib_metadata-8.7.1 ipykernel-7.2.0 ipython-9.11.0 ipython-pygments-lexers-1.1.1 jedi-0.19.2 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-4.0.0 matplotlib-inline-0.2.1 mdit-py-plugins-0.5.0 mdurl-0.1.2 myst-nb-1.4.0 myst-parser-5.0.0 nbclient-0.10.4 nbformat-5.10.4 nest-asyncio-1.6.0 parso-0.8.6 pexpect-4.9.0 platformdirs-4.9.4 prompt_toolkit-3.0.52 psutil-7.2.2 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.15.4 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+g216d96bae scanpydoc-0.17.3 six-1.17.0 soupsieve-2.8.3 sphinx-book-theme-1.1.4 sphinx-design-0.7.0 sqlalchemy-2.0.48 stack_data-0.6.3 tabulate-0.10.0 tornado-6.5.4 traitlets-5.14.3 typing-extensions-4.15.0 wcwidth-0.6.0 zipp-3.23.0

[rtd-command-info] start-time: 2026-03-09T18:05:56.534828Z, end-time: 2026-03-09T18:05:56.570349Z, 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: 2026-03-09T18:05:56.654597Z, end-time: 2026-03-09T18:06:02.652502Z, duration: 5, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v9.1.0
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
myst v5.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.4.0: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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/222/_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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reading sources... [100%] visualizing-marker-genes

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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.