What version of myst-parser are you using?

myst-parser==4.0.1

What version dependencies are you using?

Sphinx==8.2.3
myst-parser==4.0.1
myst-nb==1.3.0
sphinx-exec-code==0.16
pydata-sphinx-theme==0.16.1
sphinx-math-dollar==1.2.1

What operating system are you using?

Mac

Describe the Bug

I want to add code in my documentation using sphinx-exec-code via sphinx markdown. After everything setup I got below error.

Running Sphinx v8.2.3
loading translations [en]... done
WARNING: while setting up extension myst_nb: role 'sub-ref' is already registered and will not be overridden [app.add_role]
WARNING: while setting up extension myst_nb: directive 'figure-md' is already registered and will not be overridden [app.add_directive]

Versions

• Platform: darwin; (macOS-26.0.1-arm64-arm-64bit)
• Python version: 3.11.13 (CPython)
• Sphinx version: 8.2.3
• Docutils version: 0.21.2
• Jinja2 version: 3.1.6
• Pygments version: 2.19.2

Last Messages

None.

Loaded Extensions

None.

Traceback

  File "/Users/mymac/env/lib/python3.11/site-packages/myst_parser/sphinx_ext/main.py", line 49, in setup_sphinx
    app.registry.transforms.remove(SphinxUnreferencedFootnotesDetector)
ValueError: list.remove(x): x not in list

The full traceback has been saved in:
/var/folders/8m/7jwsmhs94td4qkl5y57tqghw0000gn/T/sphinx-err-z2hecv16.log

To report this error to the developers, please open an issue at https://github.com/sphinx-doc/sphinx/issues/. Thanks!
Please also report this if it was a user error, so that a better error message can be provided next time.
Sphinx exited with exit code: 2
The server will continue serving the build folder, but the contents being served are no longer in sync with the documentation sources. Please fix the cause of the error above or press Ctrl+C to stop the server.

Expected Behavior

No response

To Reproduce

No response