EPUB's, however, can dynamically reflow the text and resize the font to be readable on your phone, your Kindle, your PC, etc. And they're far easier to cleanly convert to other formats (even PDF, if that's your only option) than the reverse direction.
But non-fiction often includes plenty of illustrations, sidebars, images, footnotes, and so on, which while EPUB can handle in theory, often wind up with all sorts of bugs in reality, things being out of order or not making sense or being clipped instead of resized when converting to PDF, etc.
I've found PDF's to be generally more reliable overall, and not too much of a problem on my phone for average-sized book pages -- I just hold my phone in landscape mode and pinch to zoom in enough so the phone doesn't waste space on margins on the sides.
The only PDF's that doesn't work for tend to be full-size textbooks (significantly larger than the average book page), but those are also the ones where layout tends to be the most important and I've had the most disastrous experiences with EPUB. Right now I just don't think it's realistic to read most textbooks on your phone in any format. (Plus you want to highlight, annotate in the margins etc., none of which is great on the phone anyways, but is great with a stylus/pencil on your tablet.)
The problem is, every single .epub reader renders things slightly differently so when you tweak your ePub to make it look good on device A, it ends up looking bad on device B. The fixed layout of PDF is certainly restrictive, but at least it's consistent.
Context: working for past year on producing a decent quality ePub for some equation-heavy books.
Also, plug: I've available for consulting work on PDF generation (using other libraries or xtopdf, my own toolkit for PDF generation from other formats), and for PDF text extraction work. Contact info in my HN profile.
One compromise is to target a reasonable screen size in the PDF layout. Set your margins for a 6" viewable (or whatever you like to optimize for) and you should still get a reasonable experience on a tablet.
I think it is (in theory) even allowed to make an EPUB of LaTeX files, except that EPUB readers aren't required to support LaTeX (you're also allowed to provide both HTML and LaTeX, although the W3C probably expected people to use that part of the standard for audio-books).
Most commercial services these days (if my HumbleBundle books from O'Reily are any indication) simply provide pre-compiled editions in EPUB/MOBI/PDF format, as this seems to cover 95% of use cases.
It turns out there's a fair amount of tuning to make math expressions not run off the edge of the page.
On the other hand, it respects positioning, fonts, illustrations, and so on -- and is much better printed.
For narrative books I prefer EPUB all the way. Release both if possible!
It also sounds like a lot of books a proofed as a PDF (I hear a surprising amount of publishing is still driven by MS Word). Like the article says, the author may not have a version of the book with proper layout.
Either all desktop epub readers suck or the format itself is bad, but as an end user, I've never felt pleased with any epub ever. I've tried many readers, configurations, etc (I've even thought about making my own epub reader program that doesn't suck, but I haven't had any time.)
Epubs always look wrong: the formatting is all over the place, fonts look off, I don't even know what font I'm supposed to use. Calibre allows me to use CSS for styling, but I've never managed to do what I need.
I've spent many hours trying to like epub, trying to tweak Calibre so that it doesn't look like complete crap (e.g. setting good margins), but to no avail.
PDFs almost always look fine. I don't have to think about fonts, margins, etc. it just works.
> EPUB doesn't let us set a minimum length. EPUB also doesn't have line-folding glyphs. We are unlikely to release an EPUB or MOBI until they offer some way to deal with this problem.
> What big tech publishers do to get around this problem is embed low resolution jpegs of the source code in their EPUBs. This is a terrible solution and we will not put something out that does this.
> There's an e-reader formatted PDF which, on the 4 or 5 different Kindle models we've tested or seen it on, works great. No scrolling, no zooming in and out. Just works. Page turn your way through. For now, we're not going to release an EPUB.
markdown -> docx (pandoc)
docx -> kindle (calibre)
I use both pandoc and calibre as offline CLIs, and the resulting kindle book has a nicely formatted table of contents with correct chapter markers, etc.
FWIW, most of my eBook collection was purchased on Amazon before I got the Kobo, and it's been easy enough to download them all from Amazon and run them through Calibre to get them converted into an EPUB or KEPUB (special subset of EPUB that's better optimized for the Kobo) and get them onto the device.
You can go in the reverse direction as well. I regularly grab ebooks from wherever, strip away the DRM if I have to, convert to MOBI, and then email it as an attachment to the my email address associated with various family members' Kindles.