Very interesting. I was thinking of software as most similar to apparatus, and secondarily to procedure. You raise a third possible comparison: calculations,

Very interesting. I was thinking of software as most similar to apparatus, and secondarily to procedure. You raise a third possible comparison: calculations, which IIUC would be expected to be included in the paper. There are some kinds of code (a script that controls a sensor or an actuator) where I think that doesn't match up well at all. There are plenty of kinds of code where they are, in fact, simply crunching numbers produced earlier. For the latter, I'm honestly not sure the best way to treat it, except to say that we should be sure that enough information is included in some form that replication should be possible, and that we keep in mind the idea that replication should involve human interaction.