Adam Wood: actually the "they" is just me. I don't really "transcribe Gregorian Chant" - in the body of my office chants there are just a few adaptations of the original Gregorian melodies for the vernacular, the most are new "compositions".
I actually plan to code the opposite to what Ben wants: I like the output of Gregorio and the input format of LilyPond, so ly > gabc converter is what I want to have.
Better support of the chant notation in LilyPond is a complicated task - there is a testimony of the creator of Gregorio somewhere where he states that he first researched for possibilities of doing exactly this - and when he realized, how hard (if not impossible) it would be, he started the Gregorio project ...
Some time ago the possibility of converting Gregorio's input format to Lilypond's was mentioned in this discussion. So: one gabc -> lily conversion tool is here. I'm not sure how many, if any, would make any use of it. If there was such a desire, I could later, as the tool becomes more mature, create an online tool for those not willing to install and run the script on their own system.
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