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Running "calibre --ignore-plugins" fixed the problem of the window size changes not being saved for me, so I started uninstalling plugins one-by-one and it appears to be an incompatibility with Marvin XD 1.2.4. With that plugin installed, my gui.py file is not saved when calibre quits.
With Marvin XD, I get:
./calibre-debug -s
Shutdown command sent, waiting for shutdown...
/Applications/calibre.app/Contents/Resources/Python/site-packages/cherrypy/process/wspbus.py:225: RuntimeWarning: The main thread is exiting, but the Bus is in the states.STARTED state; shutting it down automatically now. You must either call bus.block() after start(), or call bus.exit() before the main thread exits.
Traceback (most recent call last):
File "site-packages/calibre/utils/Zeroconf.py", line 884, in run
File "site-packages/calibre/utils/Zeroconf.py", line 929, in handle_read
File "lib/python2.7/socket.py", line 170, in _dummy
error: [Errno 9] Bad file descriptor
Without Marvin XD, I get:
./calibre-debug -s
Shutdown command sent, waiting for shutdown...
This is on MacOS X 10.10.2, Calibre 2.20
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