This is more of a suggestion than any real issue but what ppl generally do is they highlight the software engineering aspects of their GH repos with shields on top of their README files. They are attractive, informative and eye-catching, so it might be beneficial to do the same here.
each GH Actions CI workflow generates a CI (which also changes color depending on the test status), therefore both #12 and #13 would yield one shield each.
zenodo submission also yelds a shield, so you would get one from #14
I would move the shield which points to zenodo submission with data for paper reproducibility also on the top of the README, keep it together with the previous one; in the text just provide a URL link.
check what more shields you could generate for this repo at: https://shields.io/
if you have any other ideas you can also generate custom ones with your own text, chosen colot and a custom URL.
This is more of a suggestion than any real issue but what ppl generally do is they highlight the software engineering aspects of their GH repos with shields on top of their README files. They are attractive, informative and eye-catching, so it might be beneficial to do the same here.