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A concrete instance: prms_warmup option has default of zero (in 5.2.1) but the default in pyPRMS is set 1. I have a control file without prms_warmup, round tripping the file causes output differences in the runs for runs longer than one year.
It sounds like updating the default in pyPRMS to the value in 5.2.1+ is good.
I see why populating all the control variables is desirable but it is also desirable to be able to roundtrip partial/incomplete control files. An option to do complete or maybe roundtrip mode on .init() could simply collect the keys and then delete these from the Control object before returning.