search

TransBioInfoLab / coMethDMR

Detect Regions of Concurrent Differential Methylation
https://transbioinfolab.github.io/coMethDMR/
7 stars 2 forks source link

Call all internal functions by argument and not position #18

Closed gabrielodom closed 2 years ago

gabrielodom commented 2 years ago

THIS IS NOT A BUG, YET. But, this will prevent future bugs as we continue development.

As we see in https://github.com/TransBioInfoLab/coMethDMR/issues/14 and as we saw in https://github.com/TransBioInfoLab/coMethDMR/issues/9, we may need to add arguments or change argument names (I really want to avoid the second part). If this happens, as written, our code will break. When Lissette and I drafted this code back in 2017, I was very new to package development, and I did not have her call all internal functions with named arguments. For example: f(x, y) is bad; f(arg1 = x, arg2 = y) is good. That way, if I need to insert arg1.1 between arg1 and arg2, calls to f() won't break.

gabrielodom commented 2 years ago

Currently, we have these problems in almost all internal functions, so I'm going to go through all our functions, one by one. May Christ have mercy on me.

gabrielodom commented 2 years ago

Fixed in #20