Argument naming: "assay_name" (scater) vs. "assay.type" (scuttle)

[antagomir]

We recently changed the argument name from exprs_values to assay_name in scater in PR #187 . This is in sync with mia package family, which uses assay_name as well.

The scuttle package is also using exprs_values, and I proposed a similar change in scuttle issue #21. The maintainer has decided to prefer dot arguments (assay.type) instead, and has aliases for past underscore arguments to keep the code functional.

That would be a bigger change as it would affect other arguments, too. I would be ready to consider that for mia/miaViz/miaTime/miaSim etc. packages in order to align the conventions. But that would seem to make sense only if both scater and scuttle would converge to the same. If these two packages will have different argument names, we will probably keep mia* as is, and consider additional aliases to support interoperability with both.

Just wanted to cross-check this before proceeding. Is moving to dot arguments something that the scater package could consider?

[alanocallaghan]

Sure, if you want to change from underscore to dot then try get it in before the next bioc release so I don't have to deprecate anything

[alanocallaghan]

I think this is resolved now