Warning "File Changed" in JupyterLab after reloading notebook from disk

[ser3n1ty87]

Hi!

I am using JupyterLab together with Jupytext (which is great btw) and paired one of my notebooks my-notebook.ipynb with a percent script my-notebook.py.
When I am doing bigger changes and refactoring I am usually using Vim/Neovim for modifying the my-notebook.py directly.
For getting those changes back into my my-notebook.ipynb file I am using "Reload Notebook from Disk" in JupyterLab.
This also works as expected as I can see that the code part of my .ipynb notebook (in memory) is now equivalent to the content of the .py script.
However, whenever I now want to save the .ipynb notebook to disk I get the following warning:

File Changed
"my-notebook.ipynb" has changed on disk since the last time it was opened or saved. 
Do you want to overwrite the file on disk with the version open here, or load the version on disk (revert)?

Basically, it doesn't matter if I choose to revert or overwrite then as the .ipynb file gets correctly saved.

Even though this issue is only a little inconvenience, I am wondering: Is this to be expected or am I doing something wrong here?
May it be that this warning has something to do with the timestamp which the .ipynb notebook (in memory) "inherits" when reloading from disk w.r.t. the timestamps of the ipynb notebook (on disk) and the .py script (on disk)?

[mwouts]

Hi @ser3n1ty87 , thank you for the detailed report! Well that is not expected, as you have reloaded the notebook you should not see that message. I'll try to reproduce this in a test (but I can't do this now, hopefully I'll have some time for this next week).

[mwouts]

Just a quick question, do you think you could take a note of the timestamps of each operations? I mean, timestamp of when you save the notebook in Jupyter (or timestamp of files on disk just after you do so), then the timestamp after the edit in Vim, and finally the timestamps when you get the warning in Jupyter when you try to save there? Is there any change if you exit Vim after you edit the .py file (I guess you don't have any autosave in Vim, do you?)

[ser3n1ty87]

Hi @mwouts,

sorry for the delay...
Here are the timestamps of the two files after each operation:

• initially (.py and .ipynb are paired and I saved the notebook from jupyterlab)

  • File: ‘tci_obserrstat.ipynb’
    Size: 14599781 Blocks: 28544 IO Block: 16777216 regular file
    Access: 2022-07-19 07:42:19.524311176 +0000
    Modify: 2022-07-19 07:42:19.456953000 +0000
    Change: 2022-07-19 07:42:19.456114828 +0000
  • File: ‘tci_obserrstat.py’
    Size: 15499 Blocks: 32 IO Block: 16777216 regular file
    Access: 2022-07-19 07:41:26.704664165 +0000
    Modify: 2022-07-19 07:42:19.488502000 +0000
    Change: 2022-07-19 07:42:19.487717701 +0000

• after doing some modification to .py file from vim (vim is directly closed afterwards)

  • File: ‘tci_obserrstat.ipynb’
    Size: 14599781 Blocks: 28544 IO Block: 16777216 regular file
    Access: 2022-07-19 07:42:19.524311176 +0000
    Modify: 2022-07-19 07:42:19.456953000 +0000
    Change: 2022-07-19 07:42:19.456114828 +0000
  • File: ‘tci_obserrstat.py’
    Size: 15506 Blocks: 32 IO Block: 16777216 regular file
    Access: 2022-07-19 07:46:01.222566592 +0000
    Modify: 2022-07-19 07:46:01.222394056 +0000
    Change: 2022-07-19 07:46:01.222394056 +0000

• after reloading the notebook in jupyterlab and trying to save (warning is still open)

  • File: ‘tci_obserrstat.ipynb’
    Size: 14599781 Blocks: 28544 IO Block: 16777216 regular file
    Access: 2022-07-19 07:42:19.524311176 +0000
    Modify: 2022-07-19 07:42:19.456953000 +0000
    Change: 2022-07-19 07:42:19.456114828 +0000
  • File: ‘tci_obserrstat.py’
    Size: 15506 Blocks: 32 IO Block: 16777216 regular file
    Access: 2022-07-19 07:46:01.222566592 +0000
    Modify: 2022-07-19 07:46:01.222394056 +0000
    Change: 2022-07-19 07:46:01.222394056 +0000

• after having chosen to 'overwrite' in the warning dialogue

  • File: ‘tci_obserrstat.ipynb’
    Size: 14599818 Blocks: 28544 IO Block: 16777216 regular file
    Access: 2022-07-19 07:50:24.979114805 +0000
    Modify: 2022-07-19 07:50:24.880597000 +0000
    Change: 2022-07-19 07:50:24.879923319 +0000
  • File: ‘tci_obserrstat.py’
    Size: 15506 Blocks: 32 IO Block: 16777216 regular file
    Access: 2022-07-19 07:46:01.222111000 +0000
    Modify: 2022-07-19 07:50:24.912669000 +0000
    Change: 2022-07-19 07:50:24.912201825 +0000

There also isn't any difference if I close vim or not and I also don't have any autosave configured in vim.

[mwouts]

Thank you @ser3n1ty87 for taking the time to gathering all this information ! That is really helpful. I should be able to reproduce (and fix this) in a new test. I'll keep you posted.

[mwouts]

Hi @ser3n1ty87 , I have prepared a fix for this. Would you mind giving a try to the upcoming version? You can install it with

BUILD_JUPYTERLAB_EXTENSION=1 pip install git+https://github.com/mwouts/jupytext.git@fix_978

Please let me know if that solves the issue on your end. And thank you so much for reporting this!

[ser3n1ty87]

Hi @mwouts, I just tested your fix and the issue seems to be solved now.
Thank you very much!

[mwouts]

Thank you @ser3n1ty87 for the confirmation. I'll integrate the fix and deliver a new version.

[fouronnes]

Hello,

I'm getting a bug very similar to this when using 1.16.5. Saving any notebook even right after opening makes the "File Changed" warning appear.

Downgrading to 1.16.4 fixes the issue.

edit: I will open a new issue for visibility