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A few things:

- In my case, my supervisors mostly had handwritten notes which rendered that point a bit moot. However, when I send the almost-complete draft to a professional copy editor, it was indeed a pain to add the comments. Either handwritten+scanned, as acrobat comments, or word comments, they had to be manually input into the markdown file.

- Everything else worked relatively better. It was a bit tedious to type loooong pandoc commands "pandoc --filter=... etc etc" so I recently coded pandocmk [1] to make my life easier. It's not super well documented (but it's a quite short script, so readable), but the idea is that you type the command line options as metadata at the top.

[1] https://github.com/sergiocorreia/pandocmk



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