Removing a cell in watch mode prevents redeclaring variables

[Antyos]

Describe the bug

When editing a notebook in watch mode, if I delete a cell containing a variable in an external editor while Marimo is in watch mode, Marimo prevents redefining the variable in a new cell:

This cell wasn't run because it has errors
This cell redefines variables from other cells.

'my_var' was also defined by:

• cell--1

This (annoyingly) happens if I save the file in the external editor without remembering to hit save in Marimo after defining the variable in a new cell.

Steps to reproduce:

1. Open a Marimo notebook in watch mode
2. Define a new cell with x=4, run the cell.
3. Delete the cell in an external editor and save the file. (Alternatively, if you didn't save the notebook in Marimo, just save the file again)
4. Try defining a new cell in Marimo again with x=3.

This issue is similar, but not a dupe of #1016.

Will you submit a PR?

• Yes

Environment

Details

{
  "marimo": "0.16.2",
  "editable": false,
  "location": "C:/Users/avg170002/Code/biaxial-bioreactor/code/.venv/Lib/site-packages/marimo",
  "OS": "Windows",
  "OS Version": "11",
  "Processor": "Intel64 Family 6 Model 198 Stepping 2, GenuineIntel",
  "Python Version": "3.13.6",
  "Locale": "en_US",
  "Binaries": {
    "Browser": "--",
    "Node": "v22.18.0"
  },
  "Dependencies": {
    "click": "8.2.1",
    "docutils": "0.22",
    "itsdangerous": "2.2.0",
    "jedi": "0.19.2",
    "markdown": "3.8.2",
    "narwhals": "2.2.0",
    "packaging": "25.0",
    "psutil": "7.0.0",
    "pygments": "2.19.2",
    "pymdown-extensions": "10.16.1",
    "pyyaml": "6.0.2",
    "starlette": "0.47.3",
    "tomlkit": "0.13.3",
    "typing-extensions": "4.15.0",
    "uvicorn": "0.35.0",
    "websockets": "15.0.1"
  },
  "Optional Dependencies": {
    "altair": "5.5.0",
    "duckdb": "1.3.2",
    "nbformat": "5.10.4",
    "openai": "1.102.0",
    "pandas": "2.3.2",
    "polars": "1.32.3",
    "pyarrow": "21.0.0",
    "loro": "1.5.4",
    "pytest": "8.4.1",
    "python-lsp-ruff": "2.2.2",
    "python-lsp-server": "1.13.1",
    "ruff": "0.12.11",
    "sqlglot": "27.9.0"
  },
  "Experimental Flags": {}
}

Code to reproduce

No response

[Antyos]

Why was this closed? Was this fixed by a PR?

[Antyos]

I am still able to reproduce the issue in 0.16.5. @mscolnick Do you know why this was marked as completed?

[mscolnick]

It looks like the PR was incorrectly linked. This was supposed to fix the issue but maybe does not quite handle all cases #6629

cc @dmadisetti

[dmadisetti]

Sorry about that- looks like I tagged a wrong, unrelated issue. Reopened so we can discuss, but this seems to work on my end:

bug.mp4

[Antyos]

I'm not sure what's happening in the video (the zooming makes it hard to track). I did my own screen recording showing the issue:

Recording.2025-10-05.144417.mp4

(It happens with the "Add cell" buttons too, they just didn't fit on the screen with the smaller window)

[dmadisetti]

Got you- different bug than what I fixed! Should have followed up

defining and "deleting" a cell in the external editor previously did not mutate the underlying graph, and thus prevented redefinition in a new cell. Will dig into this more, thank you for the screen share! It's much more clear now

[mscolnick]

(deleting my previous post message). I thought the concern was around overwriting/deleting that cell, but I do see the bug that you can no longer redefined the cell.

[dmadisetti]

Cool, I was able to replicate and the fix this. I would highly recommend having auto-save on with --watch. We don't really provide a mechanism for conflicts, and treat whatever is on disk as canonical. you can also add `?kiosk=true" to the notebook URL to remove all edit ability in the web interface