Markdown cells and restarting interactive window break debugger

[psomhorst]

Type: Bug

Behaviour

I have altered this bug report to reflect my newest findings.

It seems that Markdown cells (# %% [markdown] or # <markdowncell>) break the behavior of the debugger. I noticed that I was not able to reproduce the bug in short test files, but got the bug persistently in larger project files. I broke down one of my project files cell by cell, until it worked. The last cells to be removed were Markdown cells.

The debugger also break after clicking restart in the interactive window.

Steps to reproduce:

1. Create a .py file with cells deliniated with # %%, including a markdown cell, e.g.

# %% 
foo = 1
bar = 2

# %%
bar = 1
foo = 2

# %% [markdown]
""" Some _markdown_ content """

2. Set a breakpoint on a line containing code.
3. Run a code cell.
4. Click "Debug Cell" above the line containing the breakpoint.
5. The debugger will stop at the breakpoint.
6. Run the markdown cell.
7. Click "Debug cell" above the line containing the breakpoint.
8. The debugger will not stop at the breakpoint.
9. Close the interactive window.
10. Run a cell.
11. Click "Restart" in the interactive window that opened up.
12. Click "Debug Cell".
13. The debugger ignores all breakpoints.

---

(old report)

When clicking 'Debug Cell' in a Python-script containing #%% markers to deliniate cells, breakpoints are ignored in a very unpredictable way. Depending on whether the first line of a cell is to be run (jupyter.stopOnFirstLineWhileDebugging), sometimes a separate tab with a title like <ipython-input-\d-\d+> is opened, and the debugger halts on the first line. All breakpoints are ignored. In any file, when clicking 'Debug Cell' opens the interactive window (i.e., the interactive window was not opened before), the behavior seems to be as expected.
In longer files, when I first run a bunch of cells normally, debug won't work. In a short file (like the example below), it does seem to work. I can't replicate when the debugger works as expected and when it doesn't.

After restarting the kernel (using the Restart button), breakpoints are entirely ignored. Closing the interactive window resets the behavior.

Diagnostic data

launch.json configuration

{
    // Use IntelliSense to learn about possible attributes.
    // Hover to view descriptions of existing attributes.
    // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
    "version": "0.2.0",
    "configurations": [
        {
            "name": "Python Debugger: Current File",
            "type": "debugpy",
            "request": "launch",
            "program": "${file}",
            "console": "internalConsole",
            "cwd": "${workspaceFolder}",
            "justMyCode": false
        }
    ]
}

Output for Python in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Python)

2025-03-19 16:50:08.822 [info] Connecting to DAP Server at:  127.0.0.1:60310

Output for Python Debugger in the Output panel (View→Output, change the drop-down the upper-right of the Output panel to Python Debugger)

(output is empty)

Extension version: 2025.5.2025031101
VS Code version: Code 1.98.2 (Universal) (ddc367ed5c8936efe395cffeec279b04ffd7db78, 2025-03-12T13:32:45.399Z)
OS version: Darwin arm64 24.3.0
Modes:

• Python version (& distribution if applicable, e.g. Anaconda): 3.13.2
• Type of virtual environment used (e.g. conda, venv, virtualenv, etc.): VirtualEnvironment

System Info

Item	Value
CPUs	Apple M1 (8 x 2400)
GPU Status	2d_canvas: enabled canvas_oop_rasterization: enabled_on direct_rendering_display_compositor: disabled_off_ok gpu_compositing: enabled multiple_raster_threads: enabled_on opengl: enabled_on rasterization: enabled raw_draw: disabled_off_ok skia_graphite: disabled_off video_decode: enabled video_encode: enabled webgl: enabled webgl2: enabled webgpu: enabled webnn: disabled_off
Load (avg)	2, 3, 3
Memory (System)	16.00GB (0.23GB free)
Process Argv
Screen Reader	no
VM	0%

[psomhorst]

@anthonykim1 @eleanorjboyd I found some more information and changed the report significantly. Please let me know if I should create a new bug report instead.

[eleanorjboyd]

thank you for the updates- I will take a look! Sorry for the delay

[rchiodo]

This wouldn't be handled by debugpy. We don't implement debug cell. I believe that's implemented by the Jupyter extension. This is likely something to do with the dummy python files generated in the background by the Jupyter extension (that are passed to debugpy)