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multitrait changes - #531

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bhaller wants to merge 361 commits into
masterfrom
multitrait
Open

multitrait changes#531
bhaller wants to merge 361 commits into
masterfrom
multitrait

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@bhaller

@bhaller bhaller commented Jul 2, 2025

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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.

@codecov

codecov Bot commented Dec 21, 2025

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Codecov Report

❌ Patch coverage is 76.19048% with 25 lines in your changes missing coverage. Please review.
✅ Project coverage is 76.75%. Comparing base (b7d413d) to head (bb87daf).

Files with missing lines Patch % Lines
core/chromosome.cpp 76.92% 21 Missing ⚠️
core/chromosome.h 71.42% 4 Missing ⚠️
Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #531      +/-   ##
==========================================
+ Coverage   75.83%   76.75%   +0.91%     
==========================================
  Files         114      117       +3     
  Lines       72808    79312    +6504     
  Branches    12879    14423    +1544     
==========================================
+ Hits        55217    60878    +5661     
- Misses      17591    18434     +843     
Files with missing lines Coverage Δ
core/community.cpp 80.65% <ø> (+0.44%) ⬆️
core/community.h 100.00% <ø> (ø)
core/community_eidos.cpp 90.59% <ø> (-0.71%) ⬇️
core/genomic_element.cpp 68.88% <ø> (ø)
core/genomic_element.h 100.00% <ø> (ø)
core/genomic_element_type.cpp 82.62% <ø> (+0.63%) ⬆️
core/genomic_element_type.h 100.00% <ø> (ø)
core/haplosome.cpp 49.73% <ø> (+0.53%) ⬆️
core/haplosome.h 76.00% <ø> (-0.32%) ⬇️
core/chromosome.h 53.19% <71.42%> (+4.70%) ⬆️
... and 1 more

... and 79 files with indirect coverage changes

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bhaller and others added 30 commits August 15, 2026 20:39
Co-authored-by: Peter Ralph <petrel.harp@gmail.com>
put binary derived state into the mutation table metadata
error in schema and test machinery
shift the migrant flag from metadata to the flags column
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2 participants