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If you use a system tray icon the closing calibre will close to system tray. And to re-open it you need to click the system tray icon, not the dock icon. macOS does not play well with system try icons, dont use them there, just use the dock icon. As for how to automate it, you can probably use an automator script to do it, or some such. Not a macOS user, so cant be more specific than that.
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