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multitrait changes #531

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@bhaller bhaller commented Jul 2, 2025

This branch is the long-term branch for changes to implement multiple phenotypic traits in SLiM; it will likely become SLiM 5.1 or SLiM 6.0. It is is active development, and will often not build; it is not recommended for end users until further notice.

bhaller added 30 commits July 1, 2025 18:35
@bhaller
add Trait class, initializeTrait(), and related stuff
a494c45
@bhaller
add dominanceCoeff to Mutation, and related work
35c511b
@bhaller
shift MutationType's API and internals to multitrait
4341dfa
@bhaller
Merge branch 'master' into multitrait
47a15d9
@bhaller
finish the merge of master into multitrait (fix doc and project file)
814decc
@bhaller
some polish for the multitrait work already done
7a82d7a
@bhaller
fix non-breaking spaces that crept in
db483d0
@bhaller
shift to slim_effect_t instead of slim_selcoeff_t
30eb9a7
@bhaller
add support for individual offsets in Individual
27eaecc
@bhaller
fix build errors
39005f6
@bhaller
add some multitrait unit tests; fix a couple of bugs
24bd765
@bhaller
clean up the GetProperty_NO_SIGNATURE() logic a bit
72e3533
@bhaller
add Species properties for each trait in the species
58d411c
@bhaller
make code completion on dynamic trait properties work
ed77f5e
@bhaller
fix CMake EIDOS_GUI flag to fix build failure
f3e137d
@bhaller
add trait value storage and accelerated trait property get/set
4dcaf8f
@bhaller
new MutationBlock class for per-species mutation storage
9ba2211
@bhaller
fix bug in Individual trait property access
2de00ef
@bhaller
fix Trait and MutationBlock leaks
dbd38a8
@bhaller
add per-trait effect size and dominance to Substitution
167ee4a
@bhaller
trait effect/dominance properties/methods for Mutation and Substitution
f11417a
@bhaller
extend test runtime a bit to try to fix occasional failures
0875937
@bhaller
remove setSelectionCoeff(), rename selectionCoeff to effect
0629ef2
@bhaller
remove C++ selection_coeff_ and dominance_coeff_ ivars
6c1a4f9
@bhaller
add phenotypeForTrait()
5891bba
@bhaller
add setPhenotypeForTrait() method to Individual
22b5ecf
@bhaller
Merge branch 'master' into multitrait
e9aa6e3
@bhaller
update the Xcode project for the PCG RNG merge
d958550
@bhaller
initializeMutationType() sets the DES for all traits; naming shifts
e5649a9
@bhaller
shift hemizygous dominance to be a per-mutation property
0fc082f
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@bhaller