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init_state_from_founders

 init_state_from_founders (key:<function PRNGKey>,
                           founder_pop:chewc.structs.Population,
                           sp:chewc.structs.SimParam,
                           config:chewc.config.SimConfig)

Create the scan carry from a founder Population. - Keeps founders active. - Sets write_pos to the next cohort boundary.

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SimState

 SimState (geno:jax.Array, ibd:jax.Array, pheno:jax.Array, bv:jax.Array,
           is_active:jax.Array, id:jax.Array, mother:jax.Array,
           father:jax.Array, gen:jax.Array, key:<function PRNGKey>,
           write_pos:int, gen_idx:int, next_id:int)

*The dynamic state of the simulation.

This object is threaded through the generation_step function and contains all arrays and values that change from one generation to the next. Stored in the CARRY for lax.scan; It is designed to be lean and JIT-friendly.*