kepubify is a standalone tool to convert ePubs into Kobo ePubs. It does not depend on any other software such as Calibre, and runs on Windows, macOS, and Linux. It is a command line tool, but on windows, it can be used by dragging the ePub file on to kepubify. It has full support for all the main requirements of a kepub, including Kobo Spans.
kepubify also includes a tool to update the series metadata in the Kobo database based on the metadata in the epub files.
 Usage, examples, and FAQ
See the official documentation, as it is updated quite frequently.