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openjournals / joss

The Journal of Open Source Software
https://joss.theoj.org
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Internal references to sections and tables #1111

Open ulupo opened 2 years ago

ulupo commented 2 years ago

Hi! I am preparing a paper for submission to JOSS and have found some things difficult to achieve. In particular, I am unable to figure out from the submission instructions how to internally label and refer to tables and sections. Figures work just as explained in the example Markdown file, but tables and sections are not mentioned there.

I tried to follow the instructions in https://github.com/openjournals/inara/blob/main/example/paper.md (which I assumed was relevant for JOSS) but I can't even reproduce their "proglangs" table after copy+pasting from the raw file.

Furthermore, I have noticed that the command for the local Docker runs

docker run --rm \
    --volume $PWD/paper:/data \
    --user $(id -u):$(id -g) \
    --env JOURNAL=joss \
    openjournals/inara

provided in the instruction does not in fact produce identical behaviour as the GitHub action. In particular, while the local run ends in

Running filter /usr/local/share/openjournals/data/filters/self-citation.lua
Killed

in my case (to be expected perhaps because my attempts at referring to tables and sections fail), the GH action does produce a PDF, albeit with clear referencing issues ("??" or otherwise garbled references).

Thank you in advance for your help!

arfon commented 2 years ago

@tarleb – would you be able to provide some thoughts here?

tarleb commented 2 years ago

That's weird. I'll take a look, but probably not before next week.

ManavalanG commented 1 year ago

Here is the solution to reference tables - https://github.com/openjournals/docs/issues/5#issuecomment-1450525175