LSP diagnostics (Ruff) persist after fixing code

[daizutabi]

Describe the bug

LSP diagnostics (such as Ruff's "Undefined name") are not cleared and remain visible in the cell editor even after the code is fixed (e.g., changing a to a = 1).

This has been observed on Windows (Native, WSL2, devcontainer). I am not sure if this issue persists on other platforms.

1. Enter a (Error appears)	2. Change to a = 1 (Error remains)

I experimented with the code in frontend/src/core/codemirror/lsp/notebook-lsp.ts and found that the publishDiagnostics notification for clearing errors was missing the version field.

After I manually added the version field to the "clear" loop in the patchProcessNotification method, the diagnostics started clearing correctly.

However, I am not certain if this is the correct way to fix the issue.

(Update: This fix also resolved persistent diagnostics in basedpyright.)

// frontend/src/core/codemirror/lsp/notebook-lsp.ts

// ... inside patchProcessNotification's clear loop
for (const cellDocumentUri of cellsToClear) {
  previousProcessNotification({
    method: "textDocument/publishDiagnostics",
    params: {
      uri: cellDocumentUri,
      version: cellVersion, // <--- Adding this line fixed the issue
      diagnostics: [],
    },
  });
}

Will you submit a PR?

• Yes

Environment

Details

{
  "marimo": "0.20.4",
  "editable": true,
  "location": "/workspaces/marimo/marimo",
  "OS": "Linux",
  "OS Version": "6.6.87.2-microsoft-standard-WSL2",
  "Processor": "x86_64",
  "Python Version": "3.12.13",
  "Locale": "--",
  "Binaries": {
    "Browser": "--",
    "Node": "v22.22.0",
    "uv": "0.6.17"
  },
  "Dependencies": {
    "click": "8.3.1",
    "docutils": "0.22.4",
    "itsdangerous": "2.2.0",
    "jedi": "0.19.2",
    "markdown": "3.10.2",
    "narwhals": "2.17.0",
    "packaging": "26.0",
    "psutil": "7.2.2",
    "pygments": "2.19.2",
    "pymdown-extensions": "10.21",
    "pyyaml": "6.0.3",
    "starlette": "0.52.1",
    "tomlkit": "0.14.0",
    "typing-extensions": "4.15.0",
    "uvicorn": "0.41.0",
    "websockets": "16.0"
  },
  "Optional Dependencies": {
    "basedpyright": "1.38.2",
    "duckdb": "1.4.4",
    "loro": "1.10.3",
    "openai": "2.26.0",
    "pyarrow": "23.0.1",
    "pytest": "9.0.2",
    "python-lsp-ruff": "2.3.0",
    "python-lsp-server": "1.14.0",
    "ruff": "0.15.1",
    "sqlglot": "29.0.1"
  },
  "Experimental Flags": {
    "multi_column": true,
    "cache_panel": true
  }
}

Code to reproduce

1. Create a new notebook.
2. In a cell, type a.
3. Wait for the LSP (Ruff) to show an error: Undefined name 'a'.
4. Change the code to a = 1.
5. Observed Behavior: The red underline and error message for Undefined name 'a' remain in the editor.
6. Expected Behavior: The error should disappear immediately after the code becomes valid.

[mscolnick]

This might be fixed by some changes in #8390