The minimum level of disclosure that Nature Methods requires depends on how central the software is to the paper. If a software program is the focus of the report, we expect the programming code to be made available. Without this code, the software - and thus the paper - would become a black box of little use to the scientific community. In many papers, however, the software is only an ancillary part of the method, and the focus is on the methodological approach or an insight gained from it.
Nature Methods Editorial, March 2007
It's refreshing to see Nature Methods publicly acknowledge the importance of software availability in the sciences. On the other hand, the editorial still leaves wriggle room for an author determined to keep his or her source code private.
For example, consider the term "programming code." Does this mean "source code", or does it also include "object code"? The rest of the editorial makes it clear that both are acceptable to Nature Methods, although source code is preferred. Releasing binaries only "… may be acceptable if the operations performed by the software are sufficiently clear." Can any amount of description ever substitute for source code itself?
Over twenty years ago, John Figueras made the case that authors wishing to keep their source code private fundamentally misunderstood the difference between science and advertising. This may be a distinction lost on certain authors, but journals play along at their own risk.