2nd plt.figure doesn't show up with .py files and `%matplotlib ipympl`

System details:

Positron and OS details:

Positron Version: 2025.06.0 (Universal) build 167
Code - OSS Version: 1.100.0
Commit: e7e5d5590adc6bf7b760f837051cd2f57ea9e3dc
Date: 2025-05-29T20:44:08.369Z
Electron: 34.5.1
Chromium: 132.0.6834.210
Node.js: 20.19.0
V8: 13.2.152.41-electron.0
OS: Darwin arm64 23.5.0

Interpreter details:

Python 3.13.2

Describe the issue:

Take the following code and put it in a .py file:

import matplotlib.pyplot as plt
import numpy as np
plt.figure()
x = np.linspace(0, 2*np.pi, 100)
y = np.sin(3*x)
plt.plot(x, y)
plt.figure()
plt.plot(x, np.exp(3*x))

Now create a new console, run "%matplotlib ipympl" and run the file. Only the second plot shows up. If you restart the console and just copy paste this code (after running %matplotlib ipympl) it works fine, likewise if the file is renamed to .ipy instead of .py (again after running %matpl...)

Were there any error messages in the UI, Output panel, or Developer Tools console?

Not error messages, but there was a slight difference in output. Here's the output for running .py:

And here's the output for running .ipy:

It seems that in the .ipy there's two iframes getting launched, but only one for the .py

Please let me know if I can be of any further assistance.

Reproduce the issue in Positron with the provided Python code, first as a .py file and then as a .ipy file, after enabling %matplotlib ipympl. Compare how each run creates the plot output and iframes; done when both figures display for the .py case without errors.