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start at declaring traits in the slim code#1842

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petrelharp wants to merge 4 commits into
popsim-consortium:mainfrom
petrelharp:trait_mucking_around
Draft

start at declaring traits in the slim code#1842
petrelharp wants to merge 4 commits into
popsim-consortium:mainfrom
petrelharp:trait_mucking_around

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@petrelharp

@petrelharp petrelharp commented May 29, 2026

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This is a start at things - and maybe not a good start! Just trying things out.

edit: This PR has code to the following:

  1. run tests using (development) multitrait SLiM (here)
  2. initializes traits
  3. sets up mutation types and effect size distributions for traits
  4. as well as the mutation callback for multivariate traits (currently just mvn)
  5. sets individual phenotypes and implements transforms

TODOs: should be done or have an issue opened to track

@petrelharp

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Right now on my machine I get

>               raise ValueError(
                    "Invalid json+struct payload: declared lengths exceed buffer size"
                )
E               ValueError: Invalid json+struct payload: declared lengths exceed buffer size

../../../micromamba/envs/ts/lib/python3.13/site-packages/tskit/metadata.py:318: ValueError

@petrelharp petrelharp force-pushed the trait_mucking_around branch from 3dfe747 to ffcd043 Compare June 23, 2026 17:50
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