Here's something I don't understand. If I run this code:

import scadnano as sc
design = sc.Design(helices=[
    sc.Helix(max_offset=50, idx=0), 
    sc.Helix(max_offset=50, idx=2),
], grid=sc.square)
design.draw_strand(2, 8).move(-8).cross(0, move=8).move(-8)
design.write_scadnano_file('paranemic_crossover_generated.sc')

it generates this design:

Then I add this line:

design.write_cadnano_v2_file(filename='paranemic_crossover_generated.json')

and it generates this error:

ValueError: Paranemic crossovers are only allowed between helices that have the same parity of 
row number, here helix num 2 and helix num 0 
have different parity of row number: respectively 1 and 0

What's going wrong? I gave the helices indices 0 and 2 so that they have the same parity. But somehow it's getting translated to cadnano helix num of 0 and 1 instead of 0 and 2. I can fix it if I add an unused helix 1:

design = sc.Design(helices=[
    sc.Helix(max_offset=50, idx=0), 
    sc.Helix(max_offset=50, idx=1), 
    sc.Helix(max_offset=50, idx=2),
], grid=sc.square)

before drawing the strand.

Is this intended behavior? I don't remember how cadnano works. Does it disallow helix indices from being non-consecutive? (i.e., you can have helices 0,1,2,...,n but no strict subset of that?)

If so, we should probably be more specific in specifying the constraints on scadnano designs in doc/index.rst to emphasize this constraint of consecutive helix indices.

But if that's not a constraint of cadnano, then this seems like a bug in the cadnano export code, where it is looking at the helix's order in the dict Design.helices, instead of at its field Helix.idx, to generate cadnano helix num's.

I'm also confused about the distinction between scadnano helix index, and what you call num and row number in the error message. What's the difference between num and row number, and which is supposed to correspond to the field Helix.idx? I think we should also change the error message to use scadnano terms instead of cadnano terms, since we are describing a constraint on the scadnano design for it to be exportable, and scadnano designs have no concept of num or row number.

One guess I have is that by "row number", you mean the order in which the helix appears in the dict Design.helices? But it would be better to more precisely define these terms.