is there a way to select all bones from a sinlge layer including those hidden but without having to touch the state of the hidden bones?
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yes, it’s pretty simple. To select all the bones on the first layer (layers[0]), you iterate through all the bones and check if they are assigned to the layer
import bpy
for bone in bpy.context.object.data.bones:
if bone.layers[0] == True:
bone.select = True
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