Error running `jupyter-book build` right after generating my content from the template

[logankilpatrick]

I am following the getting started guide. I made a new virtual env in the same folder as my book itself and this caused things to break after 19% of the way into finishing my build. Moved the virtual env out of the folder and everything worked as expected. Maybe it is silly but I feel like with how common virtual env's are, there would be some sort of check that ensures this doesn't happen. The error message is below and gave me no inclination that the env was the issue:

(env) (base) logankilpatrick@MacBook-Pro-5 Desktop % jupyter-book build JuliaCrashCourse/
Running Jupyter-Book v0.13.1
Source Folder: /Users/logankilpatrick/Desktop/JuliaCrashCourse
Config Path: /Users/logankilpatrick/Desktop/JuliaCrashCourse/_config.yml
Output Path: /Users/logankilpatrick/Desktop/JuliaCrashCourse/_build/html
Running Sphinx v4.5.0
making output directory... done
[etoc] Changing master_doc to 'intro'
checking bibtex cache... out of date
parsing bibtex file /Users/logankilpatrick/Desktop/JuliaCrashCourse/references.bib... parsed 5 entries
myst v0.15.2: MdParserConfig(renderer='sphinx', commonmark_only=False, enable_extensions=['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist'], 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', disable_syntax=[], url_schemes=['mailto', 'http', 'https'], heading_anchors=None, heading_slug_func=None, html_meta=[], footnote_transition=True, substitutions=[], sub_delimiters=['{', '}'], words_per_minute=200)
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 151 source files that are out of date
updating environment: [new config] 151 added, 0 changed, 0 removed
reading sources... [  0%] env/lib/python3.10/site-packages/Jinja2-3.1.2.dist-infreading sources... [  1%] env/lib/python3.10/site-packages/MarkupSafe-2.1.1.distreading sources... [  1%] env/lib/python3.10/site-packages/alabaster-0.7.12.distreading sources... [  2%] env/lib/python3.10/site-packages/attrs-21.4.0.dist-infreading sources... [  3%] env/lib/python3.10/site-packages/bleach/_vendor/html5lreading sources... [  4%] env/lib/python3.10/site-packages/click-8.1.3.dist-inforeading sources... [  5%] env/lib/python3.10/site-packages/debugpy/_vendored/pydreading sources... [  5%] env/lib/python3.10/site-packages/idna-3.4.dist-info/LIreading sources... [  6%] env/lib/python3.10/site-packages/imagesize-1.4.1.dist-reading sources... [  7%] env/lib/python3.10/site-packages/ipykernel-6.16.2.distreading sources... [  7%] env/lib/python3.10/site-packages/ipython_genutils-0.2.reading sources... [  8%] env/lib/python3.10/site-packages/jupyter_book/book_temreading sources... [  9%] env/lib/python3.10/site-packages/jupyter_book/book_temreading sources... [  9%] env/lib/python3.10/site-packages/jupyter_book/book_temExecuting: env/lib/python3.10/site-packages/jupyter_book/book_template/markdown-notebooks in: /Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_book/book_template
reading sources... [ 10%] env/lib/python3.10/site-packages/jupyter_book/book_temExecuting: env/lib/python3.10/site-packages/jupyter_book/book_template/notebooks in: /Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_book/book_template
reading sources... [ 11%] env/lib/python3.10/site-packages/jupyter_client-7.4.4.reading sources... [ 11%] env/lib/python3.10/site-packages/jupyter_core-4.11.2.dreading sources... [ 12%] env/lib/python3.10/site-packages/jupyter_server-1.21.0reading sources... [ 13%] env/lib/python3.10/site-packages/jupyter_server/i18n/Rreading sources... [ 13%] env/lib/python3.10/site-packages/latexcodec-2.0.1.distreading sources... [ 14%] env/lib/python3.10/site-packages/latexcodec-2.0.1.distreading sources... [ 15%] env/lib/python3.10/site-packages/matplotlib/backends/wExecuting: env/lib/python3.10/site-packages/matplotlib/backends/web_backend/nbagg_uat in: /Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/matplotlib/backends/web_backend
reading sources... [ 15%] env/lib/python3.10/site-packages/mdit_py_plugins/contareading sources... [ 16%] env/lib/python3.10/site-packages/mdit_py_plugins/deflireading sources... [ 17%] env/lib/python3.10/site-packages/mdit_py_plugins/texmareading sources... [ 17%] env/lib/python3.10/site-packages/mistune-0.8.4.dist-inreading sources... [ 18%] env/lib/python3.10/site-packages/nbclassic/bundler/tesExecuting: env/lib/python3.10/site-packages/nbclassic/bundler/tests/resources/empty in: /Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclassic/bundler/tests/resources
reading sources... [ 19%] env/lib/python3.10/site-packages/nbclient/tests/files/Executing: env/lib/python3.10/site-packages/nbclient/tests/files/Autokill in: /Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/tests/files
/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_book/book_template/intro.md:: WARNING: tableofcontents directive in document with no descendants [etoc.tableofcontents]
/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/matplotlib/backends/web_backend/nbagg_uat.ipynb:20002: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]
/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/matplotlib/backends/web_backend/nbagg_uat.ipynb:330002: WARNING: Non-consecutive header level increase; 0 to 2 [myst.header]

Exception occurred:
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/client.py", line 953, in async_execute_cell
    raise DeadKernelError("Kernel died")
nbclient.exceptions.DeadKernelError: Kernel died
The full traceback has been saved in /var/folders/tc/519vfm453fj_x5bmd8pwx9480000gn/T/sphinx-err-b4x2rssg.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
Traceback (most recent call last):
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/client.py", line 730, in _async_poll_for_reply
    msg = await ensure_async(self.kc.shell_channel.get_msg(timeout=new_timeout))
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/util.py", line 96, in ensure_async
    result = await obj
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_client/channels.py", line 224, in get_msg
    ready = await self.socket.poll(timeout)
asyncio.exceptions.CancelledError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/client.py", line 949, in async_execute_cell
    exec_reply = await self.task_poll_for_reply
asyncio.exceptions.CancelledError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_book/sphinx.py", line 171, in build_sphinx
    app.build(force_all, filenames)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/application.py", line 330, in build
    self.builder.build_update()
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 286, in build_update
    self.build(to_build,
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 300, in build
    updated_docnames = set(self.read())
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 407, in read
    self._read_serial(docnames)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 428, in _read_serial
    self.read_doc(docname)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/builders/__init__.py", line 468, in read_doc
    doctree = read_doc(self.app, self.env, self.env.doc2path(docname))
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/io.py", line 181, in read_doc
    pub.publish()
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/docutils/core.py", line 217, in publish
    self.document = self.reader.read(self.source, self.parser,
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/sphinx/io.py", line 101, in read
    self.parse()
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/docutils/readers/__init__.py", line 78, in parse
    self.parser.parse(self.input, document)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/myst_nb/parser.py", line 67, in parse
    ntbk = generate_notebook_outputs(
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/myst_nb/execution.py", line 137, in generate_notebook_outputs
    result = single_nb_execution(
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_cache/executors/utils.py", line 51, in single_nb_execution
    executenb(
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/client.py", line 1204, in execute
    return NotebookClient(nb=nb, resources=resources, km=km, **kwargs).execute()
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/util.py", line 84, in wrapped
    return just_run(coro(*args, **kwargs))
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/util.py", line 62, in just_run
    return loop.run_until_complete(coro)
  File "/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/asyncio/base_events.py", line 641, in run_until_complete
    return future.result()
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/client.py", line 663, in async_execute
    await self.async_execute_cell(
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/nbclient/client.py", line 953, in async_execute_cell
    raise DeadKernelError("Kernel died")
nbclient.exceptions.DeadKernelError: Kernel died

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

Traceback (most recent call last):
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/bin/jupyter-book", line 8, in <module>
    sys.exit(main())
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/click/core.py", line 1130, in __call__
    return self.main(*args, **kwargs)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/click/core.py", line 1055, in main
    rv = self.invoke(ctx)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/click/core.py", line 1657, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/click/core.py", line 1404, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/click/core.py", line 760, in invoke
    return __callback(*args, **kwargs)
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_book/cli/main.py", line 323, in build
    builder_specific_actions(
  File "/Users/logankilpatrick/Desktop/JuliaCrashCourse/env/lib/python3.10/site-packages/jupyter_book/cli/main.py", line 531, in builder_specific_actions
    raise RuntimeError(_message_box(msg, color="red", doprint=False)) from result
RuntimeError: 
===============================================================================

There was an error in building your book. Look above for the cause.

===============================================================================

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[NeoNeuron]

@logankilpatrick I encountered the same issue as you did. And I fixed it by reinstalling jupyter-book using pip instead of conda.

[frankharkins]

I had a similar issue in sphinx. I think it's because Jupyter book is trying to execute notebooks from your virtual environment folder, specifically

env/lib/python3.10/site-packages/nbclient/tests/files/Autokill

which kills the kernel. I fixed mine by adding this folder to the exclude_patterns in the config:

exclude_patterns = ['env/*']

[kolibril13]

I had the same issue when .venv is in my folder, but

exclude_patterns:
  - '.venv/*'

solved this for me.

Here's the full _config.yml that fixes this issue:

# Book settings
# Learn more at https://jupyterbook.org/customize/config.html

title: My sample book
author: The Jupyter Book Community
logo: logo.png

# Force re-execution of notebooks on each build.
# See https://jupyterbook.org/content/execute.html
execute:
  execute_notebooks: force

# Define the name of the latex output file for PDF builds
latex:
  latex_documents:
    targetname: book.tex

# Add a bibtex file so that we can create citations
bibtex_bibfiles:
  - references.bib

# Information about where the book exists on the web
repository:
  url: https://github.com/executablebooks/jupyter-book  # Online location of your book
  path_to_book: docs  # Optional path to your book, relative to the repository root
  branch: master  # Which branch of the repository should be used when creating links (optional)

# Add GitHub buttons to your book
# See https://jupyterbook.org/customize/config.html#add-a-link-to-your-repository
html:
  use_issues_button: true
  use_repository_button: true

exclude_patterns:
  - '.venv/*'