Read the Docs build information
Build id: 2560711
Project: icb-scanpy-tutorials
Version: 140
Commit: 771fd370657783d65a08f61bd01c73760a6eafa2
Date: 2024-10-21T18:06:01.557308Z
State: finished
Success: True


[rtd-command-info] start-time: 2024-10-21T18:06:03.189472Z, end-time: 2024-10-21T18:06:08.843386Z, duration: 5, exit-code: 0
git clone --depth 1 https://github.com/scverse/scanpy-tutorials.git .
Cloning into '.'...

[rtd-command-info] start-time: 2024-10-21T18:06:08.963377Z, end-time: 2024-10-21T18:06:17.504372Z, duration: 8, exit-code: 0
git fetch origin --force --prune --prune-tags --depth 50 pull/140/head:external-140
From https://github.com/scverse/scanpy-tutorials
 * [new ref]         refs/pull/140/head -> external-140

[rtd-command-info] start-time: 2024-10-21T18:06:17.702639Z, end-time: 2024-10-21T18:06:18.278597Z, duration: 0, exit-code: 0
git checkout --force 771fd370657783d65a08f61bd01c73760a6eafa2
Note: switching to '771fd370657783d65a08f61bd01c73760a6eafa2'.

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 771fd37 [pre-commit.ci] pre-commit autoupdate

[rtd-command-info] start-time: 2024-10-21T18:06:18.364718Z, end-time: 2024-10-21T18:06:18.425142Z, duration: 0, exit-code: 0
cat .readthedocs.yml
version: 2
build:
  os: ubuntu-22.04
  tools:
    python: "3.12"
sphinx:
  configuration: conf.py
  fail_on_warning: true
python:
  install:
    - method: pip
      path: .

[rtd-command-info] start-time: 2024-10-21T18:06:25.153546Z, end-time: 2024-10-21T18:06:25.245552Z, duration: 0, exit-code: 0
asdf global python 3.12.3


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python -mvirtualenv $READTHEDOCS_VIRTUALENV_PATH
created virtual environment CPython3.12.3.final.0-64 in 908ms
  creator CPython3Posix(dest=/home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/envs/140, 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: 2024-10-21T18:06:27.185389Z, end-time: 2024-10-21T18:06:40.124054Z, duration: 12, 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/140/lib/python3.12/site-packages (23.1)
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Installing collected packages: setuptools, pip
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      Successfully uninstalled setuptools-67.6.1
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    Found existing installation: pip 23.1
    Uninstalling pip-23.1:
      Successfully uninstalled pip-23.1
Successfully installed pip-24.2 setuptools-75.2.0

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python -m pip install --upgrade --no-cache-dir sphinx
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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
Successfully installed Jinja2-3.1.4 MarkupSafe-3.0.2 Pygments-2.18.0 alabaster-1.0.0 babel-2.16.0 certifi-2024.8.30 charset-normalizer-3.4.0 docutils-0.21.2 idna-3.10 imagesize-1.4.1 packaging-24.1 requests-2.32.3 snowballstemmer-2.2.0 sphinx-8.1.3 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 urllib3-2.2.3

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python -m pip install --upgrade --upgrade-strategy only-if-needed --no-cache-dir .
Processing /home/docs/checkouts/readthedocs.org/user_builds/icb-scanpy-tutorials/checkouts/140
  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
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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+g771fd37-py3-none-any.whl size=990 sha256=ab7a2c2986070dd678e52c15ea8224032329d39614a4410049257b45c7e78551
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Successfully built scanpy-tutorials
Installing collected packages: wcwidth, pure-eval, ptyprocess, fastjsonschema, zipp, typing-extensions, traitlets, tornado, tabulate, soupsieve, six, rpds-py, pyzmq, pyyaml, psutil, prompt-toolkit, platformdirs, pexpect, parso, nest-asyncio, mdurl, greenlet, executing, decorator, debugpy, click, attrs, accessible-pygments, sqlalchemy, referencing, python-dateutil, matplotlib-inline, markdown-it-py, jupyter-core, jedi, importlib_metadata, comm, beautifulsoup4, asttokens, stack-data, scanpydoc, pydata-sphinx-theme, mdit-py-plugins, jupyter-client, jsonschema-specifications, sphinx-book-theme, myst-parser, jsonschema, ipython, nbformat, ipykernel, nbclient, jupyter-cache, myst-nb, scanpy-tutorials
Successfully installed accessible-pygments-0.0.5 asttokens-2.4.1 attrs-24.2.0 beautifulsoup4-4.12.3 click-8.1.7 comm-0.2.2 debugpy-1.8.7 decorator-5.1.1 executing-2.1.0 fastjsonschema-2.20.0 greenlet-3.1.1 importlib_metadata-8.5.0 ipykernel-6.29.5 ipython-8.28.0 jedi-0.19.1 jsonschema-4.23.0 jsonschema-specifications-2024.10.1 jupyter-cache-1.0.0 jupyter-client-8.6.3 jupyter-core-5.7.2 markdown-it-py-3.0.0 matplotlib-inline-0.1.7 mdit-py-plugins-0.4.2 mdurl-0.1.2 myst-nb-1.1.2 myst-parser-4.0.0 nbclient-0.10.0 nbformat-5.10.4 nest-asyncio-1.6.0 parso-0.8.4 pexpect-4.9.0 platformdirs-4.3.6 prompt-toolkit-3.0.48 psutil-6.1.0 ptyprocess-0.7.0 pure-eval-0.2.3 pydata-sphinx-theme-0.15.4 python-dateutil-2.9.0.post0 pyyaml-6.0.2 pyzmq-26.2.0 referencing-0.35.1 rpds-py-0.20.0 scanpy-tutorials-0.1.dev50+g771fd37 scanpydoc-0.14.1 six-1.16.0 soupsieve-2.6 sphinx-book-theme-1.1.3 sqlalchemy-2.0.36 stack-data-0.6.3 tabulate-0.9.0 tornado-6.4.1 traitlets-5.14.3 typing-extensions-4.12.2 wcwidth-0.2.13 zipp-3.20.2

[rtd-command-info] start-time: 2024-10-21T18:07:05.575427Z, end-time: 2024-10-21T18:07:05.641654Z, duration: 0, exit-code: 0
cat conf.py
from collections.abc import Mapping
from datetime import datetime
from importlib.metadata import metadata
from types import MappingProxyType
from typing import TYPE_CHECKING, Sequence

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

if TYPE_CHECKING:
    from docutils.parsers.rst.states import Inliner
    from sphinx.application import Sphinx


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

extensions = [
    "myst_nb",
    "sphinx.ext.intersphinx",
]
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/*",
]
pygments_style = "sphinx"

intersphinx_mapping = dict(
    scanpy=("https://scanpy.readthedocs.io/en/stable/", None),
)
# TODO: move images here from scanpy
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"]
html_css_files = ["css/custom.css"]
html_logo = "_static/img/Scanpy_Logo_BrightFG.svg"

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

nb_execution_mode = "off"
nb_output_stderr = "remove"
myst_heading_anchors = 3


# 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]]:
    msg = f"cite:{text}"
    return [
        inliner.document.reporter.info(msg),
        nodes.emphasis(rawtext, f"[{text}]"),
    ], []


class FakeDomain(Domain):
    name = "cite"
    roles = 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 AssertionError(msg)
        desc = nodes.inline("", f"{MSG}: ")
        banner = nodes.danger(
            text,
            nodes.paragraph("", "", desc, ref),
            classes=["admonition", "caution"],
        )
        return [banner]


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

[rtd-command-info] start-time: 2024-10-21T18:07:05.767933Z, end-time: 2024-10-21T18:07:16.043128Z, duration: 10, exit-code: 0
python -m sphinx -T -W --keep-going -b html -d _build/doctrees -D language=en . $READTHEDOCS_OUTPUT/html
Running Sphinx v8.1.3
loading translations [en]... done
making output directory... done
Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`.
myst v4.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions={'colon_fence'}, disable_syntax=[], all_links_external=False, links_external_new_tab=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=3, heading_slug_func=None, html_meta={}, footnote_sort=True, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
myst-nb v1.1.2: NbParserConfig(custom_formats={}, metadata_key='mystnb', cell_metadata_key='mystnb', kernel_rgx_aliases={}, eval_name_regex='^[a-zA-Z_][a-zA-Z0-9_]*$', 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, 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)
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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.