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Looks like black modified some line wraps which caused the notebook to diverge from the jupytext. I think you can either run precommit locally or modify the notebook by hand (so that black doesn't see anything to "fix") and resave. The offending line is in the pre-commit check:

"ax=az.plot_trace({\"log(tau)\": short_trace.get_values(varname=\"tau_log__\", combine=False)}, legend=True)\n"

black wants this?

"ax = az.plot_trace(\n",
"    {\"log(tau)\": short_trace.get_values(varname=\"tau_log__\", combine=False)}, legend=True\n",
")\n",

The main issue is that the notebook needs to be executed sequentially and from start to end (you can do it with the restart and run all button for example). Otherwise pre-commit will (or should) continue to fail in the "check execution order step". Notebooks are not executed so we need the outputs to be included in the ipynb file or they won't appear on the website (I wrote a bit more extended explanation on ipynb+myst duplication in #403 (comment)).

Good call. I saw that too, but wasn't sure what to make of it. @reshamas, my standard practice is to restart the jupyter kernel and rerun all cells once I am reasonably sure that my edits to a notebook are complete. That way everything is fresh and clean (until have to make more edits and then I have to rerun the entire thing again).

@OriolAbril
I am wondering if I should delete the myst file and recreate it.

Try and see if it works, it often helps. pre-commit is a bit tricky because it only runs on staged changes, so if you have unstaged changes in the repo they are ignored and it can generate more unstaged changes, worst case scenario even overwirte unstaged changes.

@reshamas It's better to delete it and execute in this order:

1. Stage the notebook
2. Run pre-commit, this will create the .myst file
3. Stage the .myst file
   $. Run pre-commit and tests should now pass

@reshamas It's better to delete it and execute in this order:

1. Stage the notebook
2. Run pre-commit, this will create the .myst file
3. Stage the .myst file
   $. Run pre-commit and tests should now pass

@symeneses I ran pre-commit and it didn't create the myst file. Not sure why. ???

Thanks for all of your help @OriolAbril !

@symeneses
It turns out I was running pre-commit on the WRONG file!!! Lesson learned. Thanks for the tip.