DeprecationWarning with Jupyterlite lab and sphinx

[MicahGale]

Description

This seems to be a dependency issue with jupyter.

Reproduce

1. Create a new conda environment with the following packages and versions:

python                          3.14.0
jupyter_client                8.6.3
jupyter_core                  5.9.1
jupyter-events                0.12.0
jupyter_server                2.17.0
jupyter_server_terminals      0.5.3
jupyterlab_pygments           0.3.0
jupyterlab_server             2.28.0
jupyterlite-core              0.6.4
jupyterlite-pyodide-kernel    0.6.1
jupyterlite-sphinx            0.22.0
jupytext                      1.18.1
lark                          1.3.1
markdown-it-py                4.0.0
MarkupSafe                    3.0.3
mdit-py-plugins               0.5.0
nbclient                      0.10.2
nbconvert                     7.16.6
nbformat                      5.10.4

2. Run jupyter lite build
3. Launch said website (I used python -m http.server)
4. Run a cell. This leads to the following warning:

/lib/python3.12/site-packages/pyodide_kernel/kernel.py:114: DeprecationWarning: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.
  if self.interpreter.should_run_async(code):

Expected behavior

Not have calls to deprecated functions.

Context

• JupyterLite version: 0.6.4
• Operating System and version: Ubuntu 25.10 with above packages.
• Browser and version: Firefox 144.0.2

Browser Output

Unsatisfied version 6.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/coreutils (required ^6.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/ui-components (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/settingregistry (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/notebook (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.5.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/apputils (required ^4.5.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/translation (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/launcher (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 7.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/services (required ^7.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/filebrowser (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/codeeditor (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/docmanager (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/rendermime (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/mainmenu (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/codemirror (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
Unsatisfied version 4.4.5 from _JUPYTERLAB.CORE_OUTPUT of shared singleton module @jupyterlab/application (required ^4.4.9) [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
No satisfying version (^4.4.9) of shared module @jupyterlab/docregistry found in shared scope default.
Available versions: 4.4.5 from _JUPYTERLAB.CORE_OUTPUT [remoteEntry.84740c0bf9a6442a86fd.js:1:5727](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/remoteEntry.84740c0bf9a6442a86fd.js)
JupyterLite ServiceWorker was already registered [service-worker-manager.js:139:21](webpack://_JUPYTERLAB.CORE_OUTPUT/packages/server/lib/service-worker-manager.js)
Disabling terminals plugin because they are not available on the server [index.js:69:17](webpack://_JUPYTERLAB.CORE_OUTPUT/node_modules/@jupyterlab/terminal-extension/lib/index.js)
JupyterLab extension jupytext is activating... [509.0926c6788335fe7dbdf8.js:1:6108](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-ipynb with rank=0 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-auto:percent with rank=1 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-auto:light with rank=2 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-auto:nomarker with rank=3 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-md with rank=4 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-md:myst with rank=5 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-Rmd with rank=6 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-qmd with rank=7 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-custom with rank=8 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering pairing command=jupytext:pair-nb-with-none with rank=9 [509.0926c6788335fe7dbdf8.js:1:7446](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering create new text notebook command=jupytext:create-new-text-notebook-md with rank=10 [509.0926c6788335fe7dbdf8.js:1:9822](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering create new text notebook command=jupytext:create-new-text-notebook-md:myst with rank=11 [509.0926c6788335fe7dbdf8.js:1:9822](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering create new text notebook command=jupytext:create-new-text-notebook-Rmd with rank=12 [509.0926c6788335fe7dbdf8.js:1:9822](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
Registering create new text notebook command=jupytext:create-new-text-notebook-qmd with rank=13 [509.0926c6788335fe7dbdf8.js:1:9822](http://127.0.0.1:8000/lite/extensions/jupyterlab-jupytext/static/509.0926c6788335fe7dbdf8.js?v=0926c6788335fe7dbdf8)
No exact match found for python, using kernel python that matches language=python [sessioncontext.js:1211:21](webpack://_JUPYTERLAB.CORE_OUTPUT/node_modules/@jupyterlab/apputils/lib/sessioncontext.js)
Pyodide contents will be synced with Jupyter Contents [index.js:92:29](webpack://jupyterlite/pyodide-kernel-extension/lib/index.js)
Starting WebSocket: ws://127.0.0.1:8000/lite/api/kernels/73be9c88-bbf2-4536-b3a3-723ef6e2f6d7 3 [default.js:69:21](webpack://_JUPYTERLAB.CORE_OUTPUT/node_modules/@jupyterlab/services/lib/kernel/default.js)
Loading micropip, packaging [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loaded micropip, packaging [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loading openssl, ssl [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loaded openssl, ssl [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loading sqlite3 [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loaded sqlite3 [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loading jedi, parso [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loaded jedi, parso [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
sqlite3 already loaded from default channel [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loading Pygments, asttokens, decorator, executing, ipython, matplotlib-inline, prompt_toolkit, pure-eval, six, stack-data, traitlets, wcwidth [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loaded Pygments, asttokens, decorator, executing, ipython, matplotlib-inline, prompt_toolkit, pure-eval, six, stack-data, traitlets, wcwidth [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loading numpy [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
Loaded numpy [352.cc74f63a8f779ace30b6.js:2:221005](http://127.0.0.1:8000/lite/extensions/@jupyterlite/pyodide-kernel-extension/static/352.cc74f63a8f779ace30b6.js?v=cc74f63a8f779ace30b6)
don't worry, about SyntaxError: JSON.parse: unexpected character at line 1 column 1 of the JSON data... nothing's broken. If there had been a
          file at http://127.0.0.1:8000/lite/api/contents/lib/python3.12/site-packages/pyodide_kernel/all.json, you might see some more files. [drive.js:849:25](webpack://_JUPYTERLAB.CORE_OUTPUT/packages/contents/lib/drive.js)
Could not resolve location of /lib/python3.12/site-packages/pyodide_kernel/kernel.py on server [registry.js:317:29](webpack://_JUPYTERLAB.CORE_OUTPUT/node_modules/@jupyterlab/rendermime/lib/registry.js)
Path resolution bailing: does not exist [renderers.js:915:25](webpack://_JUPYTERLAB.CORE_OUTPUT/node_modules/@jupyterlab/rendermime/lib/renderers.js)
​

[ManonMarchand]

I also see this warning with the last pyodide-kernel version, but only in cells which execute a request it does not occur in the first cell. I still didn't get what kind of cells trigger the warning.