I was able to solve this by switching to pycharm, for some reason spyder did not want to cooperate, kept getting DLL not found errors, "application failed could not find or load qt plugin could not be initialized", and importing QCharts would not work. everything seems to be working now thorough pycharm.
So you're right, it does appear to be a logger issue rather than a Qt one. It wasn't crashing the program at any point, but rather complaining about object cleanup order. Because of the larger structure of our code files, I couldn't assign the logger to wholely be a child of the QMainWindow, but putting the following code in the quit procedure did silence the messages.
Sorry, I figured it just failed on the last item in the list above. In any case, I just downloaded the offline version of the installer and it worked fine. This gives me a short cut to Qt Designer so I don't need the kit for Python.
OK, so the issue turned out to be something different. We are using QtPy and it needs the environment variable QT_API set to pyside2 for our Windows setup. For some reason the environment passed to QProcess isn't inheriting that variable and it was defaulting to pyside. Setting it manually to pyside2 by calling setProcessEnvironment on our QProcess before the start call gets everything working.
Not sure if this is a PySide2 bug or not. The QProcess.execute documentation says:
"The environment and working directory are inherited from the calling process."
but it doesn't say this explicitly for start.
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