Why 2 commands?

[tseemann]

Instead of 2 separate py scripts
Did you consider 2 sub-commands?

eg.
CURED main <opts>
CURED findres <opts>

[erin-thei]

Good point — I hadn’t thought about subcommands when I first wrote it. I split it into two separate scripts since they have different functionality, but I think using subcommands would make the interface cleaner and more consistent. I’ll look into refactoring it that way