Vanishing Cells in JupyterLab Notebooks

JupyterLab
1

I’ve been running into a problem with Jupyter Lab Notebooks on my Macbook

I will be adding cells (markdown or code) within a notebook (in the middle, top, or bottom) and without any predictability, the new cells or adjacent cells will disappear.

They might pop back as visible when I run the script… or they might not.
I might be able to bring them back if I click on the left margin… or they might not.

I can’t find any settings in my web browser or the jupyter notebook that could be doing this and I am using the default options.

Has anyone else seen this problem?

Much Obliged,
Bill Capehart; South Dakota School of Mines.

Details about the installation:

-- platform:       osx-arm64
-- conda version:  24.7.1
-- python version: 3.12.3.final.0
-- lead channel:   conda-forge (strict)

Jupyter/IPython Packages:

# Name                    Version                   Build  Channel
ipython                   8.26.0             pyh707e725_0    conda-forge
jupyter-lsp               2.2.5              pyhd8ed1ab_0    conda-forge
jupyter_client            8.6.2              pyhd8ed1ab_0    conda-forge
jupyter_core              5.7.2           py312h81bd7bf_0    conda-forge
jupyter_events            0.10.0             pyhd8ed1ab_0    conda-forge
jupyter_server            2.14.2             pyhd8ed1ab_0    conda-forge
jupyter_server_terminals  0.5.3              pyhd8ed1ab_0    conda-forge
jupyterlab                4.2.4              pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.3.0              pyhd8ed1ab_1    conda-forge
jupyterlab_server         2.27.3             pyhd8ed1ab_0    conda-forge
nbclient                  0.10.0             pyhd8ed1ab_0    conda-forge
nbconvert-core            7.16.4             pyhd8ed1ab_1    conda-forge
nbformat                  5.10.4             pyhd8ed1ab_0    conda-forge
2 Likes
2

I’ve seen this this week, and when I was seeing it, the main action that made cells disappear was changing the cell type to markdown. They reappeared when I started editing.

I haven’t been able to reproduce it when I look for it, so I can’t be sure of which versions were affected.

3 Likes
3

Are you all using Safari by any chance?

1 Like
4

I am, yes.

This post must be at least 20 characters

5

I wonder if this could be connected to "Add Cell" regression in 4.2.x on Safari · Issue #16373 · jupyterlab/jupyterlab · GitHub. That issue was reported as fixed in Safari Technology Preview version, so maybe testing with that version would be warranted here too?

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6

Yup, I think it’s precisely that issue, and Safari Tech Preview Release 200 (Safari 18.0, WebKit 19620.1.1) also resolves the issue for me. Thanks!

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7

Thank you all for these responses. I was indeed using Safari 17 and the problem is not seen in Chrome, for example. I look forward to the update to which Michał and “Min RK” refer.

Again, many thanks:
Bill

8

The issue is happening with chrome also

1 Like
9

The issue discussed above is not happening on Chrome. Another issue (which was fixed since) was affecting all browsers and was present in JupyterLab 4.3.1 but should be fixed in 4.3.2.

11

My cells also start to vanish on fresh installation of JH-lab when I press “a” to add cells below.

Windows 11 24H2 Windows Feature Experience Pack 1000.26100.36.0
Google Chrome Version 131.0.6778.109 (Official Build) (64-bit)
Python 3.10.0rc2
jupyter-events==0.10.0
jupyter-lsp==2.2.5
jupyter_client==8.6.3
jupyter_core==5.7.2
jupyter_server==2.14.2
jupyter_server_terminals==0.5.3
jupyterlab==4.3.1
jupyterlab_pygments==0.3.0
jupyterlab_server==2.27.3

12

jupyterlab==4.3.1

Again, the bug was largely fixed in 4.3.2. Today 4.3.3 is the latest version. Please upgrade your installation, there is no way to get bug fixes other than install patched versions.

2 Likes
13

Sorry for inattentiveness
Everything back to normal after update

2 Likes
14

I had this issue with my old notebooks after creating a new environment. It also seemed to only happen when I would try to run a cell that would output a chart or dataframe (especially larger dataframes). Most of the cells would disappear from the notebook, however changing one cell from code to markdown or vice versa would make the cells reappear. I was running 3.6.3 on old notebooks before upgrading to 4.3.3. This seemed to be the issue as 4.3.2 has not produced the issue so far.

15

@Frank_Morgan there was no relevant change in 4.3.3. Could it be that you were running 4.3.1? Could you give 4.3.3 another try?

1 Like
16

Chrome was giving me this invisible cell error - upgrading jupyterlab fixed my issue!

Successfully installed jupyterlab-4.3.4

2 Likes
17

Multiple users on a Hub I maintain are reporting vanishing cells, across multiple browsers. We are running JupyterLab 4.3.4.

The symptom is scrolling up and see a blank canvas where there should be cells, as shown. I haven’t yet been able to obtain console output that looks relevant.

image
image942×981 10.6 KB

If this seems to be a separate issue, I can open a new topic.

1 Like
18

This looks like Cells sometimes do not render when scrolling down in presence of large outputs · Issue #17023 · jupyterlab/jupyterlab · GitHub.

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19

@danielballan a reliable reproducer would mean a lot!

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20

Thank you! I will try to obtain one and post it over there.

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21

I am encountering the problem of vanishing cells with Jupyter Lab Version 4.3.5 Notebook that is rendered on Brave Browser. Every time a code cell encounters error, all the previous cells would then simply not render on the screen. I believe the “vanished cells” are still there. However, they are just not rendering (i.e. appearing). Below is a screenshot of the issue.

image
image1206×795 44.3 KB

I have to save the file, close the file and then reopen the file so that all the vanished cell can reappear. This issue is making jupyter lab notebook to be useless. It is not practical to always have to close the file and reopen the file to view all the cells.

Is there a solution to this problem?