This seems to be something to do with the PySide6 release earlier today.

I can reproduce this locally, and the timer works, is called, the quit key is triggered, and the script exits, but something appears wrong getting the close event.

FWICT, the problem seems to be mixed signals across multiple figures. The test in question has a second portion (for Agg-based backends only, which is why Cairo ones don't fail) which opens a figure to lock in the backend, then attempts to switch backends and confirm that it fails. This occurs before running the main test of opening a window, and closing it after the first draw event. In that case, the Matplotlib side does correctly close the Qt window, but the closing signal emitted through Qt seems to trigger the callback from the first figure. The first figure manager/canvas doesn't have any callbacks connected to it to print the CloseEvent, so the test fails.

Using this patch to run a copy of the test:

diff --git a/lib/matplotlib/backends/backend_qt.py b/lib/matplotlib/backends/backend_qt.py
index faeb0d6bb7..4cfa294c6e 100644
--- a/lib/matplotlib/backends/backend_qt.py
+++ b/lib/matplotlib/backends/backend_qt.py
@@ -501,6 +501,7 @@ class MainWindow(QtWidgets.QMainWindow):
     closing = QtCore.Signal()

     def closeEvent(self, event):
+        print('closeEvent', self, event, self.closing)
         self.closing.emit()
         super().closeEvent(event)

@@ -522,9 +523,11 @@ class FigureManagerQT(FigureManagerBase):
     def __init__(self, canvas, num):
         self.window = MainWindow()
         super().__init__(canvas, num)
-        self.window.closing.connect(
-            # The lambda prevents the event from being immediately gc'd.
-            lambda: CloseEvent("close_event", self.canvas)._process())
+        print('Creating new figure manager', self, canvas, num, self.window, self.window.closing)
+        def foo():
+            print('close event is happening!', self, self.canvas, self.window)
+            CloseEvent("close_event", self.canvas)._process()
+        self.window.closing.connect(foo)
         self.window.closing.connect(self._widgetclosed)

         if sys.platform != "darwin":
@@ -604,6 +607,7 @@ class FigureManagerQT(FigureManagerBase):
             self.window.raise_()

     def destroy(self, *args):
+        print('FigureManagerQT.destroy', self, self.window)
         # check for qApp first, as PySide deletes it in its atexit handler
         if QtWidgets.QApplication.instance() is None:
             return

outputs:

Creating new figure manager <matplotlib.backends.backend_qt.FigureManagerQT object at 0x7fc90fe38a60> <matplotlib.backends.backend_qtagg.FigureCanvasQTAgg(0x560b8d915020) at 0x7fc90fcc1f80> 1 <matplotlib.backends.backend_qt.MainWindow(0x560b8d91b750) at 0x7fc90fcc24c0> <PySide6.QtCore.SignalInstance closing() at 0x7fc90fffa1b0>
FigureManagerQT.destroy <matplotlib.backends.backend_qt.FigureManagerQT object at 0x7fc90fe38a60> <matplotlib.backends.backend_qt.MainWindow(0x560b8d91b750) at 0x7fc90fcc24c0>
closeEvent <matplotlib.backends.backend_qt.MainWindow(0x560b8d91b750) at 0x7fc90fcc24c0> <PySide6.QtCore.QEvent(QEvent::Close)> <PySide6.QtCore.SignalInstance closing() at 0x7fc90fffa1b0>
close event is happening! <matplotlib.backends.backend_qt.FigureManagerQT object at 0x7fc90fe38a60> <matplotlib.backends.backend_qtagg.FigureCanvasQTAgg(0x560b8d915020) at 0x7fc90fcc1f80> <matplotlib.backends.backend_qt.MainWindow(0x560b8d91b750) at 0x7fc90fcc24c0>

Creating new figure manager <matplotlib.backends.backend_qt.FigureManagerQT object at 0x7fc90d581900> <matplotlib.backends.backend_qtagg.FigureCanvasQTAgg(0x560b8d9b5ea0) at 0x7fc90d590340> 1 <matplotlib.backends.backend_qt.MainWindow(0x560b8d9e4010) at 0x7fc90d7dfd00> <PySide6.QtCore.SignalInstance closing() at 0x7fc90d715830>
FigureManagerQT.destroy <matplotlib.backends.backend_qt.FigureManagerQT object at 0x7fc90d581900> <matplotlib.backends.backend_qt.MainWindow(0x560b8d9e4010) at 0x7fc90d7dfd00>
closeEvent <matplotlib.backends.backend_qt.MainWindow(0x560b8d9e4010) at 0x7fc90d7dfd00> <PySide6.QtCore.QEvent(QEvent::Close)> <PySide6.QtCore.SignalInstance closing() at 0x7fc90d715830>
close event is happening! <matplotlib.backends.backend_qt.FigureManagerQT object at 0x7fc90fe38a60> <matplotlib.backends.backend_qtagg.FigureCanvasQTAgg(0x560b8d915020) at 0x7fc90fcc1f80> <matplotlib.backends.backend_qt.MainWindow(0x560b8d91b750) at 0x7fc90fcc24c0>

The second figure has a figure.canvas.manager of 0x7fc90d581900 and a figure.canvas.manager.window.closing instance of 0x7fc90d715830, and you can see that closeEvent receives it for that manager (so the correct window should be closed) and the same closing instance. But then when we get the callback for that signal, it's using the manager for the first window.

Looks like there's an upstream issue for this here: https://bugreports.qt.io/projects/PYSIDE/issues/PYSIDE-2346 and https://bugreports.qt.io/projects/PYSIDE/issues/PYSIDE-2348

xref for pyqtgraph also having failures on pyside 6.5.1, seems at least overlapping root cause:

pyqtgraph/pyqtgraph#2734

Ah, interesting. We have two handlers for the closing signal, one a lambda and one a method, and based on that, the former is the one having trouble. I had considered merging them together, but for some reason never tried that out yesterday.

Merging them does seem to fix the problem, so I'll try to audit all the signal connections to ensure that's the only place it's needed.

There's another case of a handler with local capture in tool manager:

(renamed to make it more discoverable as an issue since there is some conversation/notes here)