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I don't know much about ePub and its limitations. I have noticed that Ulysses (or its ePub exporter, or ePub?) falls short on all sorts of stuff that would be required for academic publishing (see all of the above).
Actually, our ePub Exporter can do most of these things, including references, footnotes, and images. Tables are currently not possible. However, we could most probably work out something to make it work (by using HTML table tags directly, since ePub are just HTML and CSS files). The online help explains most of the features already present in the Exporter.
Thank you for your comments. Here are some more thoughts of mine :)
you can't choose the style of the in-text citation. Ulysses just seems to post the [key] as the reference.
True, you can't "choose" it in the user interface. However, since the ePub Exporter is built upon the WebExport, we could convert the Exporter to a WebExport template to make it editable. From there, you could easily set up your custom citation styles (the thing is, there are countless citation styles available, so it's not really feasible to give the user a selection of different citation styles).
if you refer to the same source in different documents, Ulysses will duplicate the reference the epub output
Yes, this is something inherent with the way Documents are exported (something the Exporters can't get around easily).
you can't refer to images or tables by their number or cross-reference them.
This works definitely for images. You can write inside a paragraph something like
see also <<img>>
where the <<img>> is replaced with "Image 1" and the image is inserted after the paragraph with a caption below. Whenever you reference this image in the document, simply type <<img>>. The second image tag (<<...>>) that is not <<img>> is replaced with "Image 2".
Again, I'm not sure whether these are ePub limitations, or whether it's even Ulysses goal as an app to provide this kind of stuff.
Well, the ePub format certainly has its limitations (as I said, it's just HTML and CSS), especially with regard to scientific publications. The ePub Exporter of Ulysses tries to make as much as possible of this format and to allow the user to insert references, images, etc.
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