I have an ePub3 book involving scripting which works fine with Readium, but only partially in iBooks. My guess is that the JavaScript is erroring out at some point (although as a standard web app the exact same code works fine in Safari). Any thoughts on how to go about debugging this?
How to debug scripted ePub3 in iBooks?
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You can enable the Webkit Web Inspector in iBooks with this line in your terminal app to change its settings:
defaults write com.apple.iBooksX WebKitDeveloperExtras -bool YES
You'll find the inspector after re-starting iBooks in the context menu (More > Show Inspector). All the inspector tools are available including console etc.
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Azardi Online can be used to read the file using the browser. The built-in or add-in console can be used from there to debug. Or a console shim can be created:
References
Azardi Online
Event Handler Attributes
Debugging JavaScript on Android and iOS