Using jupytext and jupyterlab-execute-time

[marcglobality]

Cross-posting as not sure where the problem can be fixed: deshaw/jupyterlab-execute-time#15

Mainly, I would like Jupytext to ignore the execution stuff for the .py file (and in general for any extension, or at least make it configurable)

[marcglobality]

finally found the answer to this

The solution is to add a jupytext.toml to one of the places where jupytext looks for a config file. In my case:

• Create the file in ~/.config/jupytext
• Add the line default_cell_metadata_filter = "-execution"

It works for new files, not sure it will work for old ones

[mwouts]

Glad you found it! Thanks @marcglobality for sharing the answer.

I was having a look at this and at the moment it's not easy to find the default value for the cell filter. I'd like to

• improve the documentation and document explicitly the default value
• maybe include execution in the list of cell metadata that are excluded by default.

FYI the default values are found, at the moment, in this file:

jupytext/jupytext/cell_metadata.py

Lines 41 to 62 in a05ad00

	_JUPYTEXT_CELL_METADATA = [
	# Pre-jupytext metadata
	"skipline",
	"noskipline",
	# Jupytext metadata
	"cell_marker",
	"lines_to_next_cell",
	"lines_to_end_of_cell_marker",
	]
	_IGNORE_CELL_METADATA = ",".join(
	"-{}".format(name)
	for name in [
	# Frequent cell metadata that should not enter the text representation
	# (these metadata are preserved in the paired Jupyter notebook).
	"autoscroll",
	"collapsed",
	"scrolled",
	"trusted",
	"ExecuteTime",
	]
	+ _JUPYTEXT_CELL_METADATA
	)

Maybe I'll move together with the default notebook metadata filter in a default_metadata_filter.py and improve the corresponding part of the documentation. You don't mind if I reopen this issue to keep track of this?

[marcglobality]

sure, btw it seems like even having that setting, if there are execution headers in the .py, the setting gets from -execution to execution. Is this possible or I'm doing something wrong? can this be fixed?

Otherwise I'll have to fix all notebooks by hand :(

[mwouts]

btw it seems like even having that setting, if there are execution headers in the .py, the setting gets from -execution to execution. Is this possible or I'm doing something wrong? can this be fixed?

Maybe there is a bug? I'll have a look soon

Otherwise I'll have to fix all notebooks by hand :(

If you're in a hurry that may be the way to go. Rather than 'by hand', I suggest you use jupytext --update-metadata, with something like

jupytext --update-metadata '{"jupytext": {"cell_metadata_filter": "-execution"}}' *.py

[marcglobality]

nice! the latter worked great. thank you so much

[mwouts]

I am trying to wrap things up for 1.7.0. With #666 we have added execution to the list of cell metadata that are filtered by default, so I think we're done with this issue... Hopefully the new version will ship soon.

[marcglobality]

that's amazing! thanks

[mwouts]

Thank you! And, BTW, a release candidate is available at https://pypi.org/project/jupytext/1.7.0rc1/. If everything goes well the new version could ship by the end of the week.