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I was advised to use Sigil for manipulating an epub file.

My idea is to get highlighting from my Kobo ebook reader from its sqlite database and put it into the epub file so that I could see my annotations on my desktop computer.

Reading the Sigil home page I see that Sigil is an editor for epub files but I do not see how could I run a script to read the database file and put span tags to do the highlightig.

How can I program Sigil and in which programming language?

Gergely
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The Windows and macOS versions of Sigil are bundled with a Python 3 interpreter. (Linux users will have to manually install a Python 3 interpreter.) For more information on the Sigil Python API, see the Sigil Plugin Framework documentation.

If you have additional questions, you can post them in the official Sigil Plugin Delevopment thread.